SRX18362848 GSM6753787_r1 SRP409450 PRJNA904727 SRS15849306 GSM6753787 GSM6753787 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362849 GSM6753788_r1 SRP409450 PRJNA904727 SRS15849307 GSM6753788 GSM6753788 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362850 GSM6753805_r1 SRP409450 PRJNA904727 SRS15849308 GSM6753805 GSM6753805 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362851 GSM6753806_r1 SRP409450 PRJNA904727 SRS15849309 GSM6753806 GSM6753806 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362852 GSM6753807_r1 SRP409450 PRJNA904727 SRS15849310 GSM6753807 GSM6753807 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362853 GSM6753808_r1 SRP409450 PRJNA904727 SRS15849311 GSM6753808 GSM6753808 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362854 GSM6753809_r1 SRP409450 PRJNA904727 SRS15849312 GSM6753809 GSM6753809 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362855 GSM6753810_r1 SRP409450 PRJNA904727 SRS15849313 GSM6753810 GSM6753810 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362856 GSM6753811_r1 SRP409450 PRJNA904727 SRS15849314 GSM6753811 GSM6753811 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362857 GSM6753812_r1 SRP409450 PRJNA904727 SRS15849315 GSM6753812 GSM6753812 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362858 GSM6753813_r1 SRP409450 PRJNA904727 SRS15849316 GSM6753813 GSM6753813 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362859 GSM6753814_r1 SRP409450 PRJNA904727 SRS15849317 GSM6753814 GSM6753814 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362860 GSM6753815_r1 SRP409450 PRJNA904727 SRS15849318 GSM6753815 GSM6753815 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362861 GSM6753816_r1 SRP409450 PRJNA904727 SRS15849319 GSM6753816 GSM6753816 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362862 GSM6753817_r1 SRP409450 PRJNA904727 SRS15849320 GSM6753817 GSM6753817 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362863 GSM6753818_r1 SRP409450 PRJNA904727 SRS15849321 GSM6753818 GSM6753818 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362864 GSM6753819_r1 SRP409450 PRJNA904727 SRS15849322 GSM6753819 GSM6753819 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362865 GSM6753820_r1 SRP409450 PRJNA904727 SRS15849323 GSM6753820 GSM6753820 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362866 GSM6753829_r1 SRP409450 PRJNA904727 SRS15849324 GSM6753829 GSM6753829 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362867 GSM6753830_r1 SRP409450 PRJNA904727 SRS15849325 GSM6753830 GSM6753830 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362868 GSM6753831_r1 SRP409450 PRJNA904727 SRS15849326 GSM6753831 GSM6753831 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362869 GSM6753832_r1 SRP409450 PRJNA904727 SRS15849327 GSM6753832 GSM6753832 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362870 GSM6753833_r1 SRP409450 PRJNA904727 SRS15849328 GSM6753833 GSM6753833 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362871 GSM6753834_r1 SRP409450 PRJNA904727 SRS15849329 GSM6753834 GSM6753834 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362872 GSM6753835_r1 SRP409450 PRJNA904727 SRS15849330 GSM6753835 GSM6753835 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362873 GSM6753836_r1 SRP409450 PRJNA904727 SRS15849331 GSM6753836 GSM6753836 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362874 GSM6753493_r1 SRP409450 PRJNA904727 SRS15849332 GSM6753493 GSM6753493 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362875 GSM6753494_r1 SRP409450 PRJNA904727 SRS15849333 GSM6753494 GSM6753494 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362876 GSM6753495_r1 SRP409450 PRJNA904727 SRS15849334 GSM6753495 GSM6753495 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362877 GSM6753496_r1 SRP409450 PRJNA904727 SRS15849335 GSM6753496 GSM6753496 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362878 GSM6753497_r1 SRP409450 PRJNA904727 SRS15849336 GSM6753497 GSM6753497 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362879 GSM6753498_r1 SRP409450 PRJNA904727 SRS15849337 GSM6753498 GSM6753498 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362880 GSM6753499_r1 SRP409450 PRJNA904727 SRS15849338 GSM6753499 GSM6753499 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362881 GSM6753500_r1 SRP409450 PRJNA904727 SRS15849339 GSM6753500 GSM6753500 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362882 GSM6753517_r1 SRP409450 PRJNA904727 SRS15849340 GSM6753517 GSM6753517 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362883 GSM6753518_r1 SRP409450 PRJNA904727 SRS15849341 GSM6753518 GSM6753518 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362884 GSM6753519_r1 SRP409450 PRJNA904727 SRS15849342 GSM6753519 GSM6753519 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362885 GSM6753520_r1 SRP409450 PRJNA904727 SRS15849344 GSM6753520 GSM6753520 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362886 GSM6753521_r1 SRP409450 PRJNA904727 SRS15849343 GSM6753521 GSM6753521 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362887 GSM6753522_r1 SRP409450 PRJNA904727 SRS15849345 GSM6753522 GSM6753522 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362888 GSM6753523_r1 SRP409450 PRJNA904727 SRS15849346 GSM6753523 GSM6753523 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362889 GSM6753524_r1 SRP409450 PRJNA904727 SRS15849347 GSM6753524 GSM6753524 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362890 GSM6753541_r1 SRP409450 PRJNA904727 SRS15849348 GSM6753541 GSM6753541 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362891 GSM6753542_r1 SRP409450 PRJNA904727 SRS15849349 GSM6753542 GSM6753542 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362892 GSM6753543_r1 SRP409450 PRJNA904727 SRS15849350 GSM6753543 GSM6753543 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362893 GSM6753544_r1 SRP409450 PRJNA904727 SRS15849351 GSM6753544 GSM6753544 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362894 GSM6753545_r1 SRP409450 PRJNA904727 SRS15849352 GSM6753545 GSM6753545 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362895 GSM6753546_r1 SRP409450 PRJNA904727 SRS15849353 GSM6753546 GSM6753546 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362896 GSM6753547_r1 SRP409450 PRJNA904727 SRS15849354 GSM6753547 GSM6753547 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362897 GSM6753548_r1 SRP409450 PRJNA904727 SRS15849355 GSM6753548 GSM6753548 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362898 GSM6753573_r1 SRP409450 PRJNA904727 SRS15849356 GSM6753573 GSM6753573 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362899 GSM6753574_r1 SRP409450 PRJNA904727 SRS15849357 GSM6753574 GSM6753574 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362900 GSM6753575_r1 SRP409450 PRJNA904727 SRS15849358 GSM6753575 GSM6753575 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362901 GSM6753576_r1 SRP409450 PRJNA904727 SRS15849359 GSM6753576 GSM6753576 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362902 GSM6753577_r1 SRP409450 PRJNA904727 SRS15849360 GSM6753577 GSM6753577 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362903 GSM6753578_r1 SRP409450 PRJNA904727 SRS15849361 GSM6753578 GSM6753578 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362904 GSM6753579_r1 SRP409450 PRJNA904727 SRS15849362 GSM6753579 GSM6753579 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362905 GSM6753580_r1 SRP409450 PRJNA904727 SRS15849363 GSM6753580 GSM6753580 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362906 GSM6753589_r1 SRP409450 PRJNA904727 SRS15849364 GSM6753589 GSM6753589 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362907 GSM6753590_r1 SRP409450 PRJNA904727 SRS15849365 GSM6753590 GSM6753590 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362908 GSM6753591_r1 SRP409450 PRJNA904727 SRS15849367 GSM6753591 GSM6753591 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362909 GSM6753592_r1 SRP409450 PRJNA904727 SRS15849366 GSM6753592 GSM6753592 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362910 GSM6753593_r1 SRP409450 PRJNA904727 SRS15849368 GSM6753593 GSM6753593 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362911 GSM6753594_r1 SRP409450 PRJNA904727 SRS15849369 GSM6753594 GSM6753594 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362912 GSM6753595_r1 SRP409450 PRJNA904727 SRS15849370 GSM6753595 GSM6753595 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362913 GSM6753596_r1 SRP409450 PRJNA904727 SRS15849371 GSM6753596 GSM6753596 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362914 GSM6753669_r1 SRP409450 PRJNA904727 SRS15849372 GSM6753669 GSM6753669 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362915 GSM6753670_r1 SRP409450 PRJNA904727 SRS15849373 GSM6753670 GSM6753670 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362916 GSM6753671_r1 SRP409450 PRJNA904727 SRS15849374 GSM6753671 GSM6753671 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362917 GSM6753672_r1 SRP409450 PRJNA904727 SRS15849375 GSM6753672 GSM6753672 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362918 GSM6753673_r1 SRP409450 PRJNA904727 SRS15849376 GSM6753673 GSM6753673 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362919 GSM6753674_r1 SRP409450 PRJNA904727 SRS15849377 GSM6753674 GSM6753674 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362920 GSM6753675_r1 SRP409450 PRJNA904727 SRS15849378 GSM6753675 GSM6753675 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362921 GSM6753676_r1 SRP409450 PRJNA904727 SRS15849379 GSM6753676 GSM6753676 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362922 GSM6753685_r1 SRP409450 PRJNA904727 SRS15849380 GSM6753685 GSM6753685 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362923 GSM6753686_r1 SRP409450 PRJNA904727 SRS15849381 GSM6753686 GSM6753686 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362924 GSM6753687_r1 SRP409450 PRJNA904727 SRS15849382 GSM6753687 GSM6753687 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362925 GSM6753688_r1 SRP409450 PRJNA904727 SRS15849383 GSM6753688 GSM6753688 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362926 GSM6753689_r1 SRP409450 PRJNA904727 SRS15849384 GSM6753689 GSM6753689 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362927 GSM6753690_r1 SRP409450 PRJNA904727 SRS15849385 GSM6753690 GSM6753690 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362928 GSM6753691_r1 SRP409450 PRJNA904727 SRS15849386 GSM6753691 GSM6753691 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362929 GSM6753692_r1 SRP409450 PRJNA904727 SRS15849387 GSM6753692 GSM6753692 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362930 GSM6753709_r1 SRP409450 PRJNA904727 SRS15849388 GSM6753709 GSM6753709 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362931 GSM6753710_r1 SRP409450 PRJNA904727 SRS15849389 GSM6753710 GSM6753710 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362932 GSM6753711_r1 SRP409450 PRJNA904727 SRS15849390 GSM6753711 GSM6753711 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362933 GSM6753712_r1 SRP409450 PRJNA904727 SRS15849391 GSM6753712 GSM6753712 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362934 GSM6753713_r1 SRP409450 PRJNA904727 SRS15849392 GSM6753713 GSM6753713 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362935 GSM6753571_r1 SRP409450 PRJNA904727 SRS15849393 GSM6753571 GSM6753571 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362936 GSM6753572_r1 SRP409450 PRJNA904727 SRS15849394 GSM6753572 GSM6753572 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362937 GSM6753605_r1 SRP409450 PRJNA904727 SRS15849395 GSM6753605 GSM6753605 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362938 GSM6753606_r1 SRP409450 PRJNA904727 SRS15849396 GSM6753606 GSM6753606 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362939 GSM6753607_r1 SRP409450 PRJNA904727 SRS15849397 GSM6753607 GSM6753607 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362940 GSM6753608_r1 SRP409450 PRJNA904727 SRS15849399 GSM6753608 GSM6753608 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362941 GSM6753609_r1 SRP409450 PRJNA904727 SRS15849398 GSM6753609 GSM6753609 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362942 GSM6753610_r1 SRP409450 PRJNA904727 SRS15849400 GSM6753610 GSM6753610 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362943 GSM6753611_r1 SRP409450 PRJNA904727 SRS15849401 GSM6753611 GSM6753611 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362944 GSM6753612_r1 SRP409450 PRJNA904727 SRS15849402 GSM6753612 GSM6753612 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362945 GSM6753629_r1 SRP409450 PRJNA904727 SRS15849403 GSM6753629 GSM6753629 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362946 GSM6753630_r1 SRP409450 PRJNA904727 SRS15849404 GSM6753630 GSM6753630 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362947 GSM6753631_r1 SRP409450 PRJNA904727 SRS15849405 GSM6753631 GSM6753631 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362948 GSM6753632_r1 SRP409450 PRJNA904727 SRS15849406 GSM6753632 GSM6753632 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362949 GSM6753633_r1 SRP409450 PRJNA904727 SRS15849407 GSM6753633 GSM6753633 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362950 GSM6753634_r1 SRP409450 PRJNA904727 SRS15849408 GSM6753634 GSM6753634 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362951 GSM6753635_r1 SRP409450 PRJNA904727 SRS15849409 GSM6753635 GSM6753635 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362952 GSM6753636_r1 SRP409450 PRJNA904727 SRS15849410 GSM6753636 GSM6753636 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362953 GSM6753645_r1 SRP409450 PRJNA904727 SRS15849411 GSM6753645 GSM6753645 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362954 GSM6753646_r1 SRP409450 PRJNA904727 SRS15849412 GSM6753646 GSM6753646 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362955 GSM6753647_r1 SRP409450 PRJNA904727 SRS15849413 GSM6753647 GSM6753647 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362956 GSM6753648_r1 SRP409450 PRJNA904727 SRS15849414 GSM6753648 GSM6753648 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362957 GSM6753649_r1 SRP409450 PRJNA904727 SRS15849415 GSM6753649 GSM6753649 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362958 GSM6753650_r1 SRP409450 PRJNA904727 SRS15849416 GSM6753650 GSM6753650 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362959 GSM6753651_r1 SRP409450 PRJNA904727 SRS15849417 GSM6753651 GSM6753651 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362960 GSM6753652_r1 SRP409450 PRJNA904727 SRS15849418 GSM6753652 GSM6753652 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362961 GSM6753701_r1 SRP409450 PRJNA904727 SRS15849419 GSM6753701 GSM6753701 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362962 GSM6753702_r1 SRP409450 PRJNA904727 SRS15849420 GSM6753702 GSM6753702 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362963 GSM6753703_r1 SRP409450 PRJNA904727 SRS15849421 GSM6753703 GSM6753703 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362964 GSM6753704_r1 SRP409450 PRJNA904727 SRS15849422 GSM6753704 GSM6753704 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362965 GSM6753705_r1 SRP409450 PRJNA904727 SRS15849423 GSM6753705 GSM6753705 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362966 GSM6753706_r1 SRP409450 PRJNA904727 SRS15849424 GSM6753706 GSM6753706 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362967 GSM6753707_r1 SRP409450 PRJNA904727 SRS15849425 GSM6753707 GSM6753707 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362968 GSM6753708_r1 SRP409450 PRJNA904727 SRS15849426 GSM6753708 GSM6753708 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362969 GSM6753725_r1 SRP409450 PRJNA904727 SRS15849427 GSM6753725 GSM6753725 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362970 GSM6753726_r1 SRP409450 PRJNA904727 SRS15849428 GSM6753726 GSM6753726 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362971 GSM6753727_r1 SRP409450 PRJNA904727 SRS15849429 GSM6753727 GSM6753727 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362972 GSM6753728_r1 SRP409450 PRJNA904727 SRS15849430 GSM6753728 GSM6753728 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362973 GSM6753729_r1 SRP409450 PRJNA904727 SRS15849431 GSM6753729 GSM6753729 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362974 GSM6753730_r1 SRP409450 PRJNA904727 SRS15849432 GSM6753730 GSM6753730 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362975 GSM6753731_r1 SRP409450 PRJNA904727 SRS15849433 GSM6753731 GSM6753731 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362976 GSM6753732_r1 SRP409450 PRJNA904727 SRS15849434 GSM6753732 GSM6753732 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362977 GSM6753757_r1 SRP409450 PRJNA904727 SRS15849435 GSM6753757 GSM6753757 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362978 GSM6753758_r1 SRP409450 PRJNA904727 SRS15849436 GSM6753758 GSM6753758 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362979 GSM6753759_r1 SRP409450 PRJNA904727 SRS15849437 GSM6753759 GSM6753759 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362980 GSM6753760_r1 SRP409450 PRJNA904727 SRS15849438 GSM6753760 GSM6753760 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362981 GSM6753761_r1 SRP409450 PRJNA904727 SRS15849439 GSM6753761 GSM6753761 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362982 GSM6753762_r1 SRP409450 PRJNA904727 SRS15849440 GSM6753762 GSM6753762 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362983 GSM6753763_r1 SRP409450 PRJNA904727 SRS15849441 GSM6753763 GSM6753763 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362984 GSM6753764_r1 SRP409450 PRJNA904727 SRS15849442 GSM6753764 GSM6753764 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362985 GSM6753797_r1 SRP409450 PRJNA904727 SRS15849443 GSM6753797 GSM6753797 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362986 GSM6753798_r1 SRP409450 PRJNA904727 SRS15849444 GSM6753798 GSM6753798 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362987 GSM6753799_r1 SRP409450 PRJNA904727 SRS15849445 GSM6753799 GSM6753799 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362988 GSM6753800_r1 SRP409450 PRJNA904727 SRS15849446 GSM6753800 GSM6753800 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362989 GSM6753801_r1 SRP409450 PRJNA904727 SRS15849447 GSM6753801 GSM6753801 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362990 GSM6753802_r1 SRP409450 PRJNA904727 SRS15849448 GSM6753802 GSM6753802 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362991 GSM6753803_r1 SRP409450 PRJNA904727 SRS15849449 GSM6753803 GSM6753803 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362992 GSM6753804_r1 SRP409450 PRJNA904727 SRS15849450 GSM6753804 GSM6753804 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362993 GSM6753861_r1 SRP409450 PRJNA904727 SRS15849451 GSM6753861 GSM6753861 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362994 GSM6753862_r1 SRP409450 PRJNA904727 SRS15849452 GSM6753862 GSM6753862 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362995 GSM6753863_r1 SRP409450 PRJNA904727 SRS15849453 GSM6753863 GSM6753863 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362996 GSM6753864_r1 SRP409450 PRJNA904727 SRS15849454 GSM6753864 GSM6753864 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362997 GSM6753865_r1 SRP409450 PRJNA904727 SRS15849455 GSM6753865 GSM6753865 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362998 GSM6753866_r1 SRP409450 PRJNA904727 SRS15849456 GSM6753866 GSM6753866 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18362999 GSM6753867_r1 SRP409450 PRJNA904727 SRS15849457 GSM6753867 GSM6753867 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363000 GSM6753485_r1 SRP409450 PRJNA904727 SRS15849458 GSM6753485 GSM6753485 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363001 GSM6753486_r1 SRP409450 PRJNA904727 SRS15849459 GSM6753486 GSM6753486 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363002 GSM6753487_r1 SRP409450 PRJNA904727 SRS15849460 GSM6753487 GSM6753487 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363003 GSM6753488_r1 SRP409450 PRJNA904727 SRS15849461 GSM6753488 GSM6753488 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363004 GSM6753489_r1 SRP409450 PRJNA904727 SRS15849462 GSM6753489 GSM6753489 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363005 GSM6753490_r1 SRP409450 PRJNA904727 SRS15849463 GSM6753490 GSM6753490 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363006 GSM6753491_r1 SRP409450 PRJNA904727 SRS15849464 GSM6753491 GSM6753491 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363007 GSM6753492_r1 SRP409450 PRJNA904727 SRS15849465 GSM6753492 GSM6753492 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363008 GSM6753509_r1 SRP409450 PRJNA904727 SRS15849466 GSM6753509 GSM6753509 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363009 GSM6753510_r1 SRP409450 PRJNA904727 SRS15849467 GSM6753510 GSM6753510 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363010 GSM6753511_r1 SRP409450 PRJNA904727 SRS15849468 GSM6753511 GSM6753511 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363011 GSM6753512_r1 SRP409450 PRJNA904727 SRS15849469 GSM6753512 GSM6753512 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363012 GSM6753513_r1 SRP409450 PRJNA904727 SRS15849470 GSM6753513 GSM6753513 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363013 GSM6753514_r1 SRP409450 PRJNA904727 SRS15849471 GSM6753514 GSM6753514 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363014 GSM6753515_r1 SRP409450 PRJNA904727 SRS15849472 GSM6753515 GSM6753515 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363015 GSM6753516_r1 SRP409450 PRJNA904727 SRS15849473 GSM6753516 GSM6753516 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363016 GSM6753781_r1 SRP409450 PRJNA904727 SRS15849474 GSM6753781 GSM6753781 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363017 GSM6753782_r1 SRP409450 PRJNA904727 SRS15849475 GSM6753782 GSM6753782 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363018 GSM6753783_r1 SRP409450 PRJNA904727 SRS15849476 GSM6753783 GSM6753783 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363019 GSM6753784_r1 SRP409450 PRJNA904727 SRS15849477 GSM6753784 GSM6753784 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363020 GSM6753785_r1 SRP409450 PRJNA904727 SRS15849478 GSM6753785 GSM6753785 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363021 GSM6753786_r1 SRP409450 PRJNA904727 SRS15849480 GSM6753786 GSM6753786 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363022 GSM6753714_r1 SRP409450 PRJNA904727 SRS15849479 GSM6753714 GSM6753714 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363023 GSM6753715_r1 SRP409450 PRJNA904727 SRS15849481 GSM6753715 GSM6753715 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363024 GSM6753716_r1 SRP409450 PRJNA904727 SRS15849482 GSM6753716 GSM6753716 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363025 GSM6753749_r1 SRP409450 PRJNA904727 SRS15849483 GSM6753749 GSM6753749 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363026 GSM6753750_r1 SRP409450 PRJNA904727 SRS15849484 GSM6753750 GSM6753750 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363027 GSM6753751_r1 SRP409450 PRJNA904727 SRS15849485 GSM6753751 GSM6753751 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363028 GSM6753752_r1 SRP409450 PRJNA904727 SRS15849486 GSM6753752 GSM6753752 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363029 GSM6753753_r1 SRP409450 PRJNA904727 SRS15849487 GSM6753753 GSM6753753 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363030 GSM6753754_r1 SRP409450 PRJNA904727 SRS15849488 GSM6753754 GSM6753754 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363031 GSM6753755_r1 SRP409450 PRJNA904727 SRS15849489 GSM6753755 GSM6753755 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363032 GSM6753756_r1 SRP409450 PRJNA904727 SRS15849490 GSM6753756 GSM6753756 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363033 GSM6753773_r1 SRP409450 PRJNA904727 SRS15849491 GSM6753773 GSM6753773 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363034 GSM6753774_r1 SRP409450 PRJNA904727 SRS15849492 GSM6753774 GSM6753774 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363035 GSM6753775_r1 SRP409450 PRJNA904727 SRS15849493 GSM6753775 GSM6753775 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363036 GSM6753776_r1 SRP409450 PRJNA904727 SRS15849494 GSM6753776 GSM6753776 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363037 GSM6753777_r1 SRP409450 PRJNA904727 SRS15849495 GSM6753777 GSM6753777 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363038 GSM6753778_r1 SRP409450 PRJNA904727 SRS15849496 GSM6753778 GSM6753778 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363039 GSM6753779_r1 SRP409450 PRJNA904727 SRS15849497 GSM6753779 GSM6753779 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363040 GSM6753780_r1 SRP409450 PRJNA904727 SRS15849498 GSM6753780 GSM6753780 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363041 GSM6753845_r1 SRP409450 PRJNA904727 SRS15849499 GSM6753845 GSM6753845 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363042 GSM6753846_r1 SRP409450 PRJNA904727 SRS15849500 GSM6753846 GSM6753846 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363043 GSM6753847_r1 SRP409450 PRJNA904727 SRS15849501 GSM6753847 GSM6753847 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363044 GSM6753848_r1 SRP409450 PRJNA904727 SRS15849502 GSM6753848 GSM6753848 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363045 GSM6753849_r1 SRP409450 PRJNA904727 SRS15849503 GSM6753849 GSM6753849 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363046 GSM6753850_r1 SRP409450 PRJNA904727 SRS15849504 GSM6753850 GSM6753850 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363047 GSM6753851_r1 SRP409450 PRJNA904727 SRS15849505 GSM6753851 GSM6753851 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363048 GSM6753852_r1 SRP409450 PRJNA904727 SRS15849506 GSM6753852 GSM6753852 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363049 GSM6753501_r1 SRP409450 PRJNA904727 SRS15849507 GSM6753501 GSM6753501 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363050 GSM6753502_r1 SRP409450 PRJNA904727 SRS15849508 GSM6753502 GSM6753502 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363051 GSM6753503_r1 SRP409450 PRJNA904727 SRS15849509 GSM6753503 GSM6753503 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363052 GSM6753504_r1 SRP409450 PRJNA904727 SRS15849510 GSM6753504 GSM6753504 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363053 GSM6753505_r1 SRP409450 PRJNA904727 SRS15849511 GSM6753505 GSM6753505 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363054 GSM6753506_r1 SRP409450 PRJNA904727 SRS15849512 GSM6753506 GSM6753506 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363055 GSM6753507_r1 SRP409450 PRJNA904727 SRS15849513 GSM6753507 GSM6753507 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363056 GSM6753508_r1 SRP409450 PRJNA904727 SRS15849514 GSM6753508 GSM6753508 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363057 GSM6753533_r1 SRP409450 PRJNA904727 SRS15849515 GSM6753533 GSM6753533 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363058 GSM6753534_r1 SRP409450 PRJNA904727 SRS15849516 GSM6753534 GSM6753534 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363059 GSM6753535_r1 SRP409450 PRJNA904727 SRS15849517 GSM6753535 GSM6753535 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363060 GSM6753536_r1 SRP409450 PRJNA904727 SRS15849518 GSM6753536 GSM6753536 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363061 GSM6753537_r1 SRP409450 PRJNA904727 SRS15849519 GSM6753537 GSM6753537 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363062 GSM6753538_r1 SRP409450 PRJNA904727 SRS15849520 GSM6753538 GSM6753538 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363063 GSM6753539_r1 SRP409450 PRJNA904727 SRS15849521 GSM6753539 GSM6753539 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363064 GSM6753540_r1 SRP409450 PRJNA904727 SRS15849522 GSM6753540 GSM6753540 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363065 GSM6753557_r1 SRP409450 PRJNA904727 SRS15849523 GSM6753557 GSM6753557 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363066 GSM6753558_r1 SRP409450 PRJNA904727 SRS15849524 GSM6753558 GSM6753558 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363067 GSM6753559_r1 SRP409450 PRJNA904727 SRS15849525 GSM6753559 GSM6753559 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363068 GSM6753560_r1 SRP409450 PRJNA904727 SRS15849526 GSM6753560 GSM6753560 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363069 GSM6753561_r1 SRP409450 PRJNA904727 SRS15849527 GSM6753561 GSM6753561 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363070 GSM6753562_r1 SRP409450 PRJNA904727 SRS15849528 GSM6753562 GSM6753562 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363071 GSM6753563_r1 SRP409450 PRJNA904727 SRS15849529 GSM6753563 GSM6753563 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363072 GSM6753564_r1 SRP409450 PRJNA904727 SRS15849530 GSM6753564 GSM6753564 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363073 GSM6753581_r1 SRP409450 PRJNA904727 SRS15849531 GSM6753581 GSM6753581 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363074 GSM6753582_r1 SRP409450 PRJNA904727 SRS15849532 GSM6753582 GSM6753582 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363075 GSM6753583_r1 SRP409450 PRJNA904727 SRS15849537 GSM6753583 GSM6753583 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363076 GSM6753584_r1 SRP409450 PRJNA904727 SRS15849533 GSM6753584 GSM6753584 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363077 GSM6753585_r1 SRP409450 PRJNA904727 SRS15849534 GSM6753585 GSM6753585 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363078 GSM6753586_r1 SRP409450 PRJNA904727 SRS15849535 GSM6753586 GSM6753586 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363079 GSM6753587_r1 SRP409450 PRJNA904727 SRS15849536 GSM6753587 GSM6753587 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363080 GSM6753588_r1 SRP409450 PRJNA904727 SRS15849538 GSM6753588 GSM6753588 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363081 GSM6753597_r1 SRP409450 PRJNA904727 SRS15849539 GSM6753597 GSM6753597 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363082 GSM6753598_r1 SRP409450 PRJNA904727 SRS15849540 GSM6753598 GSM6753598 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363083 GSM6753599_r1 SRP409450 PRJNA904727 SRS15849541 GSM6753599 GSM6753599 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363084 GSM6753600_r1 SRP409450 PRJNA904727 SRS15849542 GSM6753600 GSM6753600 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363085 GSM6753601_r1 SRP409450 PRJNA904727 SRS15849543 GSM6753601 GSM6753601 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363086 GSM6753602_r1 SRP409450 PRJNA904727 SRS15849544 GSM6753602 GSM6753602 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363087 GSM6753603_r1 SRP409450 PRJNA904727 SRS15849545 GSM6753603 GSM6753603 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363088 GSM6753604_r1 SRP409450 PRJNA904727 SRS15849546 GSM6753604 GSM6753604 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363089 GSM6753613_r1 SRP409450 PRJNA904727 SRS15849547 GSM6753613 GSM6753613 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363090 GSM6753614_r1 SRP409450 PRJNA904727 SRS15849548 GSM6753614 GSM6753614 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363091 GSM6753615_r1 SRP409450 PRJNA904727 SRS15849549 GSM6753615 GSM6753615 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363092 GSM6753616_r1 SRP409450 PRJNA904727 SRS15849550 GSM6753616 GSM6753616 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363093 GSM6753617_r1 SRP409450 PRJNA904727 SRS15849551 GSM6753617 GSM6753617 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363094 GSM6753618_r1 SRP409450 PRJNA904727 SRS15849552 GSM6753618 GSM6753618 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363095 GSM6753619_r1 SRP409450 PRJNA904727 SRS15849553 GSM6753619 GSM6753619 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363096 GSM6753620_r1 SRP409450 PRJNA904727 SRS15849555 GSM6753620 GSM6753620 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363097 GSM6753621_r1 SRP409450 PRJNA904727 SRS15849554 GSM6753621 GSM6753621 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363098 GSM6753622_r1 SRP409450 PRJNA904727 SRS15849556 GSM6753622 GSM6753622 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363099 GSM6753623_r1 SRP409450 PRJNA904727 SRS15849559 GSM6753623 GSM6753623 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363100 GSM6753624_r1 SRP409450 PRJNA904727 SRS15849557 GSM6753624 GSM6753624 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363101 GSM6753625_r1 SRP409450 PRJNA904727 SRS15849558 GSM6753625 GSM6753625 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363102 GSM6753626_r1 SRP409450 PRJNA904727 SRS15849560 GSM6753626 GSM6753626 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363103 GSM6753627_r1 SRP409450 PRJNA904727 SRS15849561 GSM6753627 GSM6753627 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363104 GSM6753628_r1 SRP409450 PRJNA904727 SRS15849562 GSM6753628 GSM6753628 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363105 GSM6753637_r1 SRP409450 PRJNA904727 SRS15849563 GSM6753637 GSM6753637 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363106 GSM6753638_r1 SRP409450 PRJNA904727 SRS15849564 GSM6753638 GSM6753638 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363107 GSM6753639_r1 SRP409450 PRJNA904727 SRS15849565 GSM6753639 GSM6753639 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363108 GSM6753640_r1 SRP409450 PRJNA904727 SRS15849566 GSM6753640 GSM6753640 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363109 GSM6753641_r1 SRP409450 PRJNA904727 SRS15849567 GSM6753641 GSM6753641 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363110 GSM6753642_r1 SRP409450 PRJNA904727 SRS15849568 GSM6753642 GSM6753642 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363111 GSM6753643_r1 SRP409450 PRJNA904727 SRS15849569 GSM6753643 GSM6753643 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363112 GSM6753644_r1 SRP409450 PRJNA904727 SRS15849570 GSM6753644 GSM6753644 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363113 GSM6753661_r1 SRP409450 PRJNA904727 SRS15849573 GSM6753661 GSM6753661 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363114 GSM6753662_r1 SRP409450 PRJNA904727 SRS15849571 GSM6753662 GSM6753662 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363115 GSM6753663_r1 SRP409450 PRJNA904727 SRS15849572 GSM6753663 GSM6753663 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363116 GSM6753664_r1 SRP409450 PRJNA904727 SRS15849576 GSM6753664 GSM6753664 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363117 GSM6753665_r1 SRP409450 PRJNA904727 SRS15849574 GSM6753665 GSM6753665 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363118 GSM6753666_r1 SRP409450 PRJNA904727 SRS15849575 GSM6753666 GSM6753666 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363119 GSM6753667_r1 SRP409450 PRJNA904727 SRS15849577 GSM6753667 GSM6753667 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363120 GSM6753668_r1 SRP409450 PRJNA904727 SRS15849578 GSM6753668 GSM6753668 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363121 GSM6753677_r1 SRP409450 PRJNA904727 SRS15849579 GSM6753677 GSM6753677 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363122 GSM6753678_r1 SRP409450 PRJNA904727 SRS15849580 GSM6753678 GSM6753678 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363123 GSM6753679_r1 SRP409450 PRJNA904727 SRS15849581 GSM6753679 GSM6753679 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363124 GSM6753680_r1 SRP409450 PRJNA904727 SRS15849582 GSM6753680 GSM6753680 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363125 GSM6753681_r1 SRP409450 PRJNA904727 SRS15849583 GSM6753681 GSM6753681 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363126 GSM6753682_r1 SRP409450 PRJNA904727 SRS15849584 GSM6753682 GSM6753682 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363127 GSM6753683_r1 SRP409450 PRJNA904727 SRS15849585 GSM6753683 GSM6753683 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363128 GSM6753684_r1 SRP409450 PRJNA904727 SRS15849586 GSM6753684 GSM6753684 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363129 GSM6753717_r1 SRP409450 PRJNA904727 SRS15849587 GSM6753717 GSM6753717 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363130 GSM6753718_r1 SRP409450 PRJNA904727 SRS15849588 GSM6753718 GSM6753718 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363131 GSM6753719_r1 SRP409450 PRJNA904727 SRS15849590 GSM6753719 GSM6753719 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363132 GSM6753720_r1 SRP409450 PRJNA904727 SRS15849589 GSM6753720 GSM6753720 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363133 GSM6753721_r1 SRP409450 PRJNA904727 SRS15849591 GSM6753721 GSM6753721 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363134 GSM6753722_r1 SRP409450 PRJNA904727 SRS15849592 GSM6753722 GSM6753722 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363135 GSM6753723_r1 SRP409450 PRJNA904727 SRS15849593 GSM6753723 GSM6753723 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363136 GSM6753724_r1 SRP409450 PRJNA904727 SRS15849594 GSM6753724 GSM6753724 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363137 GSM6753741_r1 SRP409450 PRJNA904727 SRS15849595 GSM6753741 GSM6753741 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363138 GSM6753742_r1 SRP409450 PRJNA904727 SRS15849596 GSM6753742 GSM6753742 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363139 GSM6753743_r1 SRP409450 PRJNA904727 SRS15849597 GSM6753743 GSM6753743 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363140 GSM6753744_r1 SRP409450 PRJNA904727 SRS15849598 GSM6753744 GSM6753744 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363141 GSM6753745_r1 SRP409450 PRJNA904727 SRS15849599 GSM6753745 GSM6753745 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363142 GSM6753746_r1 SRP409450 PRJNA904727 SRS15849600 GSM6753746 GSM6753746 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363143 GSM6753747_r1 SRP409450 PRJNA904727 SRS15849601 GSM6753747 GSM6753747 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363144 GSM6753748_r1 SRP409450 PRJNA904727 SRS15849602 GSM6753748 GSM6753748 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363145 GSM6753484_r1 SRP409450 PRJNA904727 SRS15849603 GSM6753484 GSM6753484 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363146 GSM6753525_r1 SRP409450 PRJNA904727 SRS15849604 GSM6753525 GSM6753525 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363147 GSM6753526_r1 SRP409450 PRJNA904727 SRS15849605 GSM6753526 GSM6753526 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363148 GSM6753527_r1 SRP409450 PRJNA904727 SRS15849606 GSM6753527 GSM6753527 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363149 GSM6753528_r1 SRP409450 PRJNA904727 SRS15849607 GSM6753528 GSM6753528 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363150 GSM6753529_r1 SRP409450 PRJNA904727 SRS15849608 GSM6753529 GSM6753529 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363151 GSM6753530_r1 SRP409450 PRJNA904727 SRS15849609 GSM6753530 GSM6753530 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363152 GSM6753531_r1 SRP409450 PRJNA904727 SRS15849611 GSM6753531 GSM6753531 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363153 GSM6753532_r1 SRP409450 PRJNA904727 SRS15849610 GSM6753532 GSM6753532 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363154 GSM6753549_r1 SRP409450 PRJNA904727 SRS15849612 GSM6753549 GSM6753549 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363155 GSM6753550_r1 SRP409450 PRJNA904727 SRS15849613 GSM6753550 GSM6753550 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363156 GSM6753551_r1 SRP409450 PRJNA904727 SRS15849614 GSM6753551 GSM6753551 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363157 GSM6753552_r1 SRP409450 PRJNA904727 SRS15849615 GSM6753552 GSM6753552 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363158 GSM6753553_r1 SRP409450 PRJNA904727 SRS15849616 GSM6753553 GSM6753553 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363159 GSM6753554_r1 SRP409450 PRJNA904727 SRS15849617 GSM6753554 GSM6753554 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363160 GSM6753555_r1 SRP409450 PRJNA904727 SRS15849618 GSM6753555 GSM6753555 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363161 GSM6753556_r1 SRP409450 PRJNA904727 SRS15849619 GSM6753556 GSM6753556 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363162 GSM6753653_r1 SRP409450 PRJNA904727 SRS15849620 GSM6753653 GSM6753653 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363163 GSM6753654_r1 SRP409450 PRJNA904727 SRS15849622 GSM6753654 GSM6753654 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363164 GSM6753655_r1 SRP409450 PRJNA904727 SRS15849621 GSM6753655 GSM6753655 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363165 GSM6753656_r1 SRP409450 PRJNA904727 SRS15849623 GSM6753656 GSM6753656 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363166 GSM6753657_r1 SRP409450 PRJNA904727 SRS15849624 GSM6753657 GSM6753657 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363167 GSM6753658_r1 SRP409450 PRJNA904727 SRS15849625 GSM6753658 GSM6753658 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363168 GSM6753659_r1 SRP409450 PRJNA904727 SRS15849626 GSM6753659 GSM6753659 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363169 GSM6753660_r1 SRP409450 PRJNA904727 SRS15849627 GSM6753660 GSM6753660 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363170 GSM6753693_r1 SRP409450 PRJNA904727 SRS15849628 GSM6753693 GSM6753693 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363171 GSM6753694_r1 SRP409450 PRJNA904727 SRS15849629 GSM6753694 GSM6753694 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363172 GSM6753695_r1 SRP409450 PRJNA904727 SRS15849630 GSM6753695 GSM6753695 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363173 GSM6753696_r1 SRP409450 PRJNA904727 SRS15849631 GSM6753696 GSM6753696 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363174 GSM6753697_r1 SRP409450 PRJNA904727 SRS15849632 GSM6753697 GSM6753697 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363175 GSM6753698_r1 SRP409450 PRJNA904727 SRS15849633 GSM6753698 GSM6753698 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363176 GSM6753699_r1 SRP409450 PRJNA904727 SRS15849634 GSM6753699 GSM6753699 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363177 GSM6753700_r1 SRP409450 PRJNA904727 SRS15849635 GSM6753700 GSM6753700 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363178 GSM6753733_r1 SRP409450 PRJNA904727 SRS15849637 GSM6753733 GSM6753733 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363179 GSM6753734_r1 SRP409450 PRJNA904727 SRS15849636 GSM6753734 GSM6753734 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363180 GSM6753735_r1 SRP409450 PRJNA904727 SRS15849638 GSM6753735 GSM6753735 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363181 GSM6753736_r1 SRP409450 PRJNA904727 SRS15849639 GSM6753736 GSM6753736 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363182 GSM6753737_r1 SRP409450 PRJNA904727 SRS15849640 GSM6753737 GSM6753737 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363183 GSM6753738_r1 SRP409450 PRJNA904727 SRS15849641 GSM6753738 GSM6753738 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363184 GSM6753739_r1 SRP409450 PRJNA904727 SRS15849642 GSM6753739 GSM6753739 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363185 GSM6753740_r1 SRP409450 PRJNA904727 SRS15849643 GSM6753740 GSM6753740 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363186 GSM6753765_r1 SRP409450 PRJNA904727 SRS15849644 GSM6753765 GSM6753765 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363187 GSM6753766_r1 SRP409450 PRJNA904727 SRS15849645 GSM6753766 GSM6753766 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363188 GSM6753767_r1 SRP409450 PRJNA904727 SRS15849646 GSM6753767 GSM6753767 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363189 GSM6753768_r1 SRP409450 PRJNA904727 SRS15849647 GSM6753768 GSM6753768 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363190 GSM6753769_r1 SRP409450 PRJNA904727 SRS15849648 GSM6753769 GSM6753769 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363191 GSM6753770_r1 SRP409450 PRJNA904727 SRS15849649 GSM6753770 GSM6753770 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363192 GSM6753771_r1 SRP409450 PRJNA904727 SRS15849650 GSM6753771 GSM6753771 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363193 GSM6753772_r1 SRP409450 PRJNA904727 SRS15849652 GSM6753772 GSM6753772 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363194 GSM6753789_r1 SRP409450 PRJNA904727 SRS15849651 GSM6753789 GSM6753789 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363195 GSM6753790_r1 SRP409450 PRJNA904727 SRS15849653 GSM6753790 GSM6753790 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363196 GSM6753791_r1 SRP409450 PRJNA904727 SRS15849654 GSM6753791 GSM6753791 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363197 GSM6753792_r1 SRP409450 PRJNA904727 SRS15849658 GSM6753792 GSM6753792 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363198 GSM6753793_r1 SRP409450 PRJNA904727 SRS15849655 GSM6753793 GSM6753793 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363199 GSM6753794_r1 SRP409450 PRJNA904727 SRS15849656 GSM6753794 GSM6753794 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363200 GSM6753795_r1 SRP409450 PRJNA904727 SRS15849657 GSM6753795 GSM6753795 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363201 GSM6753796_r1 SRP409450 PRJNA904727 SRS15849659 GSM6753796 GSM6753796 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363202 GSM6753821_r1 SRP409450 PRJNA904727 SRS15849660 GSM6753821 GSM6753821 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363203 GSM6753822_r1 SRP409450 PRJNA904727 SRS15849661 GSM6753822 GSM6753822 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363204 GSM6753823_r1 SRP409450 PRJNA904727 SRS15849662 GSM6753823 GSM6753823 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363205 GSM6753824_r1 SRP409450 PRJNA904727 SRS15849663 GSM6753824 GSM6753824 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363206 GSM6753825_r1 SRP409450 PRJNA904727 SRS15849664 GSM6753825 GSM6753825 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363207 GSM6753826_r1 SRP409450 PRJNA904727 SRS15849665 GSM6753826 GSM6753826 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363208 GSM6753827_r1 SRP409450 PRJNA904727 SRS15849666 GSM6753827 GSM6753827 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363209 GSM6753828_r1 SRP409450 PRJNA904727 SRS15849667 GSM6753828 GSM6753828 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363210 GSM6753837_r1 SRP409450 PRJNA904727 SRS15849668 GSM6753837 GSM6753837 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363211 GSM6753838_r1 SRP409450 PRJNA904727 SRS15849669 GSM6753838 GSM6753838 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363212 GSM6753839_r1 SRP409450 PRJNA904727 SRS15849670 GSM6753839 GSM6753839 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363213 GSM6753840_r1 SRP409450 PRJNA904727 SRS15849672 GSM6753840 GSM6753840 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363214 GSM6753841_r1 SRP409450 PRJNA904727 SRS15849671 GSM6753841 GSM6753841 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363215 GSM6753842_r1 SRP409450 PRJNA904727 SRS15849673 GSM6753842 GSM6753842 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363216 GSM6753843_r1 SRP409450 PRJNA904727 SRS15849674 GSM6753843 GSM6753843 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363217 GSM6753844_r1 SRP409450 PRJNA904727 SRS15849675 GSM6753844 GSM6753844 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363218 GSM6753853_r1 SRP409450 PRJNA904727 SRS15849676 GSM6753853 GSM6753853 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363219 GSM6753854_r1 SRP409450 PRJNA904727 SRS15849677 GSM6753854 GSM6753854 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363220 GSM6753855_r1 SRP409450 PRJNA904727 SRS15849678 GSM6753855 GSM6753855 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363221 GSM6753856_r1 SRP409450 PRJNA904727 SRS15849679 GSM6753856 GSM6753856 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363222 GSM6753857_r1 SRP409450 PRJNA904727 SRS15849680 GSM6753857 GSM6753857 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363223 GSM6753858_r1 SRP409450 PRJNA904727 SRS15849681 GSM6753858 GSM6753858 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363224 GSM6753859_r1 SRP409450 PRJNA904727 SRS15849682 GSM6753859 GSM6753859 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363225 GSM6753860_r1 SRP409450 PRJNA904727 SRS15849683 GSM6753860 GSM6753860 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363226 GSM6753565_r1 SRP409450 PRJNA904727 SRS15849684 GSM6753565 GSM6753565 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363227 GSM6753566_r1 SRP409450 PRJNA904727 SRS15849685 GSM6753566 GSM6753566 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363228 GSM6753567_r1 SRP409450 PRJNA904727 SRS15849686 GSM6753567 GSM6753567 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363229 GSM6753568_r1 SRP409450 PRJNA904727 SRS15849688 GSM6753568 GSM6753568 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363230 GSM6753569_r1 SRP409450 PRJNA904727 SRS15849687 GSM6753569 GSM6753569 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000 SRX18363231 GSM6753570_r1 SRP409450 PRJNA904727 SRS15849689 GSM6753570 GSM6753570 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer's recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer's recommendation using 100ng total RNA as input per sample. cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer's recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio NextSeq 2000