SRX2228627 GSM2338941 SRP090981 PRJNA347285 SRS1732818 SAMN05878575 RNA-Seq TRANSCRIPTOMIC cDNA Briefly, RNA was obtained using the Ambion RNAqeous kit (LifeTechnologies), with a pretreatment using 250 μl lysozyme (50 mg/ml final; Sigma) and 125 μl mutanolysin (1000 units/ml; Sigma), at 37˚C for 10 min. Total RNA was immediately subjected to DNase treatment with the Turbo DNase free (Ambion) using 3 μl of DNase I for 1 hour at 37º C. RNA integrity was checked in a Bioanalyzer using an Agilent RNA Nano Chip, with a minimal RIN (RNA Integrity Number) of 7. Genomic DNA contamination was evaluated by qPCR and universal bacterial primers Uni334F and Uni514R53. Ribosomal RNA depletion was achieved using the Ribo-Zero magnetic kit Bacteria (Epicentre, Madison WA). Manufacturer instructions were followed (using 28 or 26 μl of RNA depending on the concentration). mRNA was purified with the Qiagen RNeasy Minelute Cleanup kit, following the instructions presented in the Ribo-Zero protocol for this part. RNA was eluted in 13 µl. One μl of the RNA was checked for removal of 16S and 23S rRNA peaks using the Qubit HS RNA Assay (Agilent). Chromatograms were manually inspected. Messenger RNA was finally converted to cDNA. For first strand cDNA synthesis, the Superscript II Reverse Transcriptase was used (Invitrogen) and second cDNA strand was synthesized using the NEBNext mRNA Second Strand Synthesis Module (New England Biolabs, Ipswich, MA). Then, the MinElute Reaction Cleanup Kit (Qiagen, Valencia CA) was used for cleaning up the DNA. cDNA was quantified using the Qubit High Sensitivity DNA kit (Life Technologies), and fragmented in a Bioruptor (Diagenode). An average fragment length of 300-500 bp was desired for next steps. Sequencing libraries were prepared using the BiooScientific NEXTflex Chip Seq Kit (Bioo Scientific, Austin TX). This kit is Illumina compatible. Ten ng of fragmented cDNA were used. In the manufacturer protocol, option 3 was followed entirely, with the goal to select fragments between 300 and 400 bp in a gel-free protocol. Size selection and clean-up steps were achieved using the Agencourt Ampure XP beads (Beckman Coulter, Brea CA), and a Magnetic Stand-96 (LifeTechnologies). All temperature-sensitive reactions were carried out in a preheated thermocycler. Adapters used (NEXTflex™ ChIP-Seq Barcodes, Bioo Scientific) contained 6-bp indexes for multiplexing. At the last step, ligation products were amplified by PCR with the supplied reagents for 17 cycles. Pooled libraries were sequenced on an Illumina HiSeq 2500. Sequencing was run for 50 cycles, with read length of 50 bp (single reads). Illumina HiSeq 2500 gds 302338941 GSM2338941 GEO Accession GSM2338941 SRX2228628 GSM2338942 SRP090981 PRJNA347285 SRS1732819 SAMN05878574 RNA-Seq TRANSCRIPTOMIC cDNA Briefly, RNA was obtained using the Ambion RNAqeous kit (LifeTechnologies), with a pretreatment using 250 μl lysozyme (50 mg/ml final; Sigma) and 125 μl mutanolysin (1000 units/ml; Sigma), at 37˚C for 10 min. Total RNA was immediately subjected to DNase treatment with the Turbo DNase free (Ambion) using 3 μl of DNase I for 1 hour at 37º C. RNA integrity was checked in a Bioanalyzer using an Agilent RNA Nano Chip, with a minimal RIN (RNA Integrity Number) of 7. Genomic DNA contamination was evaluated by qPCR and universal bacterial primers Uni334F and Uni514R53. Ribosomal RNA depletion was achieved using the Ribo-Zero magnetic kit Bacteria (Epicentre, Madison WA). Manufacturer instructions were followed (using 28 or 26 μl of RNA depending on the concentration). mRNA was purified with the Qiagen RNeasy Minelute Cleanup kit, following the instructions presented in the Ribo-Zero protocol for this part. RNA was eluted in 13 µl. One μl of the RNA was checked for removal of 16S and 23S rRNA peaks using the Qubit HS RNA Assay (Agilent). Chromatograms were manually inspected. Messenger RNA was finally converted to cDNA. For first strand cDNA synthesis, the Superscript II Reverse Transcriptase was used (Invitrogen) and second cDNA strand was synthesized using the NEBNext mRNA Second Strand Synthesis Module (New England Biolabs, Ipswich, MA). Then, the MinElute Reaction Cleanup Kit (Qiagen, Valencia CA) was used for cleaning up the DNA. cDNA was quantified using the Qubit High Sensitivity DNA kit (Life Technologies), and fragmented in a Bioruptor (Diagenode). An average fragment length of 300-500 bp was desired for next steps. Sequencing libraries were prepared using the BiooScientific NEXTflex Chip Seq Kit (Bioo Scientific, Austin TX). This kit is Illumina compatible. Ten ng of fragmented cDNA were used. In the manufacturer protocol, option 3 was followed entirely, with the goal to select fragments between 300 and 400 bp in a gel-free protocol. Size selection and clean-up steps were achieved using the Agencourt Ampure XP beads (Beckman Coulter, Brea CA), and a Magnetic Stand-96 (LifeTechnologies). All temperature-sensitive reactions were carried out in a preheated thermocycler. Adapters used (NEXTflex™ ChIP-Seq Barcodes, Bioo Scientific) contained 6-bp indexes for multiplexing. At the last step, ligation products were amplified by PCR with the supplied reagents for 17 cycles. Pooled libraries were sequenced on an Illumina HiSeq 2500. Sequencing was run for 50 cycles, with read length of 50 bp (single reads). Illumina HiSeq 2500 gds 302338942 GSM2338942 GEO Accession GSM2338942 SRX2228629 GSM2338943 SRP090981 PRJNA347285 SRS1732820 SAMN05878573 RNA-Seq TRANSCRIPTOMIC cDNA Briefly, RNA was obtained using the Ambion RNAqeous kit (LifeTechnologies), with a pretreatment using 250 μl lysozyme (50 mg/ml final; Sigma) and 125 μl mutanolysin (1000 units/ml; Sigma), at 37˚C for 10 min. Total RNA was immediately subjected to DNase treatment with the Turbo DNase free (Ambion) using 3 μl of DNase I for 1 hour at 37º C. RNA integrity was checked in a Bioanalyzer using an Agilent RNA Nano Chip, with a minimal RIN (RNA Integrity Number) of 7. Genomic DNA contamination was evaluated by qPCR and universal bacterial primers Uni334F and Uni514R53. Ribosomal RNA depletion was achieved using the Ribo-Zero magnetic kit Bacteria (Epicentre, Madison WA). Manufacturer instructions were followed (using 28 or 26 μl of RNA depending on the concentration). mRNA was purified with the Qiagen RNeasy Minelute Cleanup kit, following the instructions presented in the Ribo-Zero protocol for this part. RNA was eluted in 13 µl. One μl of the RNA was checked for removal of 16S and 23S rRNA peaks using the Qubit HS RNA Assay (Agilent). Chromatograms were manually inspected. Messenger RNA was finally converted to cDNA. For first strand cDNA synthesis, the Superscript II Reverse Transcriptase was used (Invitrogen) and second cDNA strand was synthesized using the NEBNext mRNA Second Strand Synthesis Module (New England Biolabs, Ipswich, MA). Then, the MinElute Reaction Cleanup Kit (Qiagen, Valencia CA) was used for cleaning up the DNA. cDNA was quantified using the Qubit High Sensitivity DNA kit (Life Technologies), and fragmented in a Bioruptor (Diagenode). An average fragment length of 300-500 bp was desired for next steps. Sequencing libraries were prepared using the BiooScientific NEXTflex Chip Seq Kit (Bioo Scientific, Austin TX). This kit is Illumina compatible. Ten ng of fragmented cDNA were used. In the manufacturer protocol, option 3 was followed entirely, with the goal to select fragments between 300 and 400 bp in a gel-free protocol. Size selection and clean-up steps were achieved using the Agencourt Ampure XP beads (Beckman Coulter, Brea CA), and a Magnetic Stand-96 (LifeTechnologies). All temperature-sensitive reactions were carried out in a preheated thermocycler. Adapters used (NEXTflex™ ChIP-Seq Barcodes, Bioo Scientific) contained 6-bp indexes for multiplexing. At the last step, ligation products were amplified by PCR with the supplied reagents for 17 cycles. Pooled libraries were sequenced on an Illumina HiSeq 2500. Sequencing was run for 50 cycles, with read length of 50 bp (single reads). Illumina HiSeq 2500 gds 302338943 GSM2338943 GEO Accession GSM2338943 SRX2228630 GSM2338944 SRP090981 PRJNA347285 SRS1732821 SAMN05878572 RNA-Seq TRANSCRIPTOMIC cDNA Briefly, RNA was obtained using the Ambion RNAqeous kit (LifeTechnologies), with a pretreatment using 250 μl lysozyme (50 mg/ml final; Sigma) and 125 μl mutanolysin (1000 units/ml; Sigma), at 37˚C for 10 min. Total RNA was immediately subjected to DNase treatment with the Turbo DNase free (Ambion) using 3 μl of DNase I for 1 hour at 37º C. RNA integrity was checked in a Bioanalyzer using an Agilent RNA Nano Chip, with a minimal RIN (RNA Integrity Number) of 7. Genomic DNA contamination was evaluated by qPCR and universal bacterial primers Uni334F and Uni514R53. Ribosomal RNA depletion was achieved using the Ribo-Zero magnetic kit Bacteria (Epicentre, Madison WA). Manufacturer instructions were followed (using 28 or 26 μl of RNA depending on the concentration). mRNA was purified with the Qiagen RNeasy Minelute Cleanup kit, following the instructions presented in the Ribo-Zero protocol for this part. RNA was eluted in 13 µl. One μl of the RNA was checked for removal of 16S and 23S rRNA peaks using the Qubit HS RNA Assay (Agilent). Chromatograms were manually inspected. Messenger RNA was finally converted to cDNA. For first strand cDNA synthesis, the Superscript II Reverse Transcriptase was used (Invitrogen) and second cDNA strand was synthesized using the NEBNext mRNA Second Strand Synthesis Module (New England Biolabs, Ipswich, MA). Then, the MinElute Reaction Cleanup Kit (Qiagen, Valencia CA) was used for cleaning up the DNA. cDNA was quantified using the Qubit High Sensitivity DNA kit (Life Technologies), and fragmented in a Bioruptor (Diagenode). An average fragment length of 300-500 bp was desired for next steps. Sequencing libraries were prepared using the BiooScientific NEXTflex Chip Seq Kit (Bioo Scientific, Austin TX). This kit is Illumina compatible. Ten ng of fragmented cDNA were used. In the manufacturer protocol, option 3 was followed entirely, with the goal to select fragments between 300 and 400 bp in a gel-free protocol. Size selection and clean-up steps were achieved using the Agencourt Ampure XP beads (Beckman Coulter, Brea CA), and a Magnetic Stand-96 (LifeTechnologies). All temperature-sensitive reactions were carried out in a preheated thermocycler. Adapters used (NEXTflex™ ChIP-Seq Barcodes, Bioo Scientific) contained 6-bp indexes for multiplexing. At the last step, ligation products were amplified by PCR with the supplied reagents for 17 cycles. Pooled libraries were sequenced on an Illumina HiSeq 2500. Sequencing was run for 50 cycles, with read length of 50 bp (single reads). Illumina HiSeq 2500 gds 302338944 GSM2338944 GEO Accession GSM2338944 SRX2228631 GSM2338945 SRP090981 PRJNA347285 SRS1732822 SAMN05878589 RNA-Seq TRANSCRIPTOMIC cDNA Briefly, RNA was obtained using the Ambion RNAqeous kit (LifeTechnologies), with a pretreatment using 250 μl lysozyme (50 mg/ml final; Sigma) and 125 μl mutanolysin (1000 units/ml; Sigma), at 37˚C for 10 min. Total RNA was immediately subjected to DNase treatment with the Turbo DNase free (Ambion) using 3 μl of DNase I for 1 hour at 37º C. RNA integrity was checked in a Bioanalyzer using an Agilent RNA Nano Chip, with a minimal RIN (RNA Integrity Number) of 7. Genomic DNA contamination was evaluated by qPCR and universal bacterial primers Uni334F and Uni514R53. Ribosomal RNA depletion was achieved using the Ribo-Zero magnetic kit Bacteria (Epicentre, Madison WA). Manufacturer instructions were followed (using 28 or 26 μl of RNA depending on the concentration). mRNA was purified with the Qiagen RNeasy Minelute Cleanup kit, following the instructions presented in the Ribo-Zero protocol for this part. RNA was eluted in 13 µl. One μl of the RNA was checked for removal of 16S and 23S rRNA peaks using the Qubit HS RNA Assay (Agilent). Chromatograms were manually inspected. Messenger RNA was finally converted to cDNA. For first strand cDNA synthesis, the Superscript II Reverse Transcriptase was used (Invitrogen) and second cDNA strand was synthesized using the NEBNext mRNA Second Strand Synthesis Module (New England Biolabs, Ipswich, MA). Then, the MinElute Reaction Cleanup Kit (Qiagen, Valencia CA) was used for cleaning up the DNA. cDNA was quantified using the Qubit High Sensitivity DNA kit (Life Technologies), and fragmented in a Bioruptor (Diagenode). An average fragment length of 300-500 bp was desired for next steps. Sequencing libraries were prepared using the BiooScientific NEXTflex Chip Seq Kit (Bioo Scientific, Austin TX). This kit is Illumina compatible. Ten ng of fragmented cDNA were used. In the manufacturer protocol, option 3 was followed entirely, with the goal to select fragments between 300 and 400 bp in a gel-free protocol. Size selection and clean-up steps were achieved using the Agencourt Ampure XP beads (Beckman Coulter, Brea CA), and a Magnetic Stand-96 (LifeTechnologies). All temperature-sensitive reactions were carried out in a preheated thermocycler. Adapters used (NEXTflex™ ChIP-Seq Barcodes, Bioo Scientific) contained 6-bp indexes for multiplexing. At the last step, ligation products were amplified by PCR with the supplied reagents for 17 cycles. Pooled libraries were sequenced on an Illumina HiSeq 2500. Sequencing was run for 50 cycles, with read length of 50 bp (single reads). Illumina HiSeq 2500 gds 302338945 GSM2338945 GEO Accession GSM2338945 SRX2228632 GSM2338946 SRP090981 PRJNA347285 SRS1732823 SAMN05878588 RNA-Seq TRANSCRIPTOMIC cDNA Briefly, RNA was obtained using the Ambion RNAqeous kit (LifeTechnologies), with a pretreatment using 250 μl lysozyme (50 mg/ml final; Sigma) and 125 μl mutanolysin (1000 units/ml; Sigma), at 37˚C for 10 min. Total RNA was immediately subjected to DNase treatment with the Turbo DNase free (Ambion) using 3 μl of DNase I for 1 hour at 37º C. RNA integrity was checked in a Bioanalyzer using an Agilent RNA Nano Chip, with a minimal RIN (RNA Integrity Number) of 7. Genomic DNA contamination was evaluated by qPCR and universal bacterial primers Uni334F and Uni514R53. Ribosomal RNA depletion was achieved using the Ribo-Zero magnetic kit Bacteria (Epicentre, Madison WA). Manufacturer instructions were followed (using 28 or 26 μl of RNA depending on the concentration). mRNA was purified with the Qiagen RNeasy Minelute Cleanup kit, following the instructions presented in the Ribo-Zero protocol for this part. RNA was eluted in 13 µl. One μl of the RNA was checked for removal of 16S and 23S rRNA peaks using the Qubit HS RNA Assay (Agilent). Chromatograms were manually inspected. Messenger RNA was finally converted to cDNA. For first strand cDNA synthesis, the Superscript II Reverse Transcriptase was used (Invitrogen) and second cDNA strand was synthesized using the NEBNext mRNA Second Strand Synthesis Module (New England Biolabs, Ipswich, MA). Then, the MinElute Reaction Cleanup Kit (Qiagen, Valencia CA) was used for cleaning up the DNA. cDNA was quantified using the Qubit High Sensitivity DNA kit (Life Technologies), and fragmented in a Bioruptor (Diagenode). An average fragment length of 300-500 bp was desired for next steps. Sequencing libraries were prepared using the BiooScientific NEXTflex Chip Seq Kit (Bioo Scientific, Austin TX). This kit is Illumina compatible. Ten ng of fragmented cDNA were used. In the manufacturer protocol, option 3 was followed entirely, with the goal to select fragments between 300 and 400 bp in a gel-free protocol. Size selection and clean-up steps were achieved using the Agencourt Ampure XP beads (Beckman Coulter, Brea CA), and a Magnetic Stand-96 (LifeTechnologies). All temperature-sensitive reactions were carried out in a preheated thermocycler. Adapters used (NEXTflex™ ChIP-Seq Barcodes, Bioo Scientific) contained 6-bp indexes for multiplexing. At the last step, ligation products were amplified by PCR with the supplied reagents for 17 cycles. Pooled libraries were sequenced on an Illumina HiSeq 2500. Sequencing was run for 50 cycles, with read length of 50 bp (single reads). Illumina HiSeq 2500 gds 302338946 GSM2338946 GEO Accession GSM2338946 SRX2228633 GSM2338947 SRP090981 PRJNA347285 SRS1732824 SAMN05878587 RNA-Seq TRANSCRIPTOMIC cDNA Briefly, RNA was obtained using the Ambion RNAqeous kit (LifeTechnologies), with a pretreatment using 250 μl lysozyme (50 mg/ml final; Sigma) and 125 μl mutanolysin (1000 units/ml; Sigma), at 37˚C for 10 min. Total RNA was immediately subjected to DNase treatment with the Turbo DNase free (Ambion) using 3 μl of DNase I for 1 hour at 37º C. RNA integrity was checked in a Bioanalyzer using an Agilent RNA Nano Chip, with a minimal RIN (RNA Integrity Number) of 7. Genomic DNA contamination was evaluated by qPCR and universal bacterial primers Uni334F and Uni514R53. Ribosomal RNA depletion was achieved using the Ribo-Zero magnetic kit Bacteria (Epicentre, Madison WA). Manufacturer instructions were followed (using 28 or 26 μl of RNA depending on the concentration). mRNA was purified with the Qiagen RNeasy Minelute Cleanup kit, following the instructions presented in the Ribo-Zero protocol for this part. RNA was eluted in 13 µl. One μl of the RNA was checked for removal of 16S and 23S rRNA peaks using the Qubit HS RNA Assay (Agilent). Chromatograms were manually inspected. Messenger RNA was finally converted to cDNA. For first strand cDNA synthesis, the Superscript II Reverse Transcriptase was used (Invitrogen) and second cDNA strand was synthesized using the NEBNext mRNA Second Strand Synthesis Module (New England Biolabs, Ipswich, MA). Then, the MinElute Reaction Cleanup Kit (Qiagen, Valencia CA) was used for cleaning up the DNA. cDNA was quantified using the Qubit High Sensitivity DNA kit (Life Technologies), and fragmented in a Bioruptor (Diagenode). An average fragment length of 300-500 bp was desired for next steps. Sequencing libraries were prepared using the BiooScientific NEXTflex Chip Seq Kit (Bioo Scientific, Austin TX). This kit is Illumina compatible. Ten ng of fragmented cDNA were used. In the manufacturer protocol, option 3 was followed entirely, with the goal to select fragments between 300 and 400 bp in a gel-free protocol. Size selection and clean-up steps were achieved using the Agencourt Ampure XP beads (Beckman Coulter, Brea CA), and a Magnetic Stand-96 (LifeTechnologies). All temperature-sensitive reactions were carried out in a preheated thermocycler. Adapters used (NEXTflex™ ChIP-Seq Barcodes, Bioo Scientific) contained 6-bp indexes for multiplexing. At the last step, ligation products were amplified by PCR with the supplied reagents for 17 cycles. Pooled libraries were sequenced on an Illumina HiSeq 2500. Sequencing was run for 50 cycles, with read length of 50 bp (single reads). Illumina HiSeq 2500 gds 302338947 GSM2338947 GEO Accession GSM2338947 SRX2228634 GSM2338948 SRP090981 PRJNA347285 SRS1732825 SAMN05878586 RNA-Seq TRANSCRIPTOMIC cDNA Briefly, RNA was obtained using the Ambion RNAqeous kit (LifeTechnologies), with a pretreatment using 250 μl lysozyme (50 mg/ml final; Sigma) and 125 μl mutanolysin (1000 units/ml; Sigma), at 37˚C for 10 min. Total RNA was immediately subjected to DNase treatment with the Turbo DNase free (Ambion) using 3 μl of DNase I for 1 hour at 37º C. RNA integrity was checked in a Bioanalyzer using an Agilent RNA Nano Chip, with a minimal RIN (RNA Integrity Number) of 7. Genomic DNA contamination was evaluated by qPCR and universal bacterial primers Uni334F and Uni514R53. Ribosomal RNA depletion was achieved using the Ribo-Zero magnetic kit Bacteria (Epicentre, Madison WA). Manufacturer instructions were followed (using 28 or 26 μl of RNA depending on the concentration). mRNA was purified with the Qiagen RNeasy Minelute Cleanup kit, following the instructions presented in the Ribo-Zero protocol for this part. RNA was eluted in 13 µl. One μl of the RNA was checked for removal of 16S and 23S rRNA peaks using the Qubit HS RNA Assay (Agilent). Chromatograms were manually inspected. Messenger RNA was finally converted to cDNA. For first strand cDNA synthesis, the Superscript II Reverse Transcriptase was used (Invitrogen) and second cDNA strand was synthesized using the NEBNext mRNA Second Strand Synthesis Module (New England Biolabs, Ipswich, MA). Then, the MinElute Reaction Cleanup Kit (Qiagen, Valencia CA) was used for cleaning up the DNA. cDNA was quantified using the Qubit High Sensitivity DNA kit (Life Technologies), and fragmented in a Bioruptor (Diagenode). An average fragment length of 300-500 bp was desired for next steps. Sequencing libraries were prepared using the BiooScientific NEXTflex Chip Seq Kit (Bioo Scientific, Austin TX). This kit is Illumina compatible. Ten ng of fragmented cDNA were used. In the manufacturer protocol, option 3 was followed entirely, with the goal to select fragments between 300 and 400 bp in a gel-free protocol. Size selection and clean-up steps were achieved using the Agencourt Ampure XP beads (Beckman Coulter, Brea CA), and a Magnetic Stand-96 (LifeTechnologies). All temperature-sensitive reactions were carried out in a preheated thermocycler. Adapters used (NEXTflex™ ChIP-Seq Barcodes, Bioo Scientific) contained 6-bp indexes for multiplexing. At the last step, ligation products were amplified by PCR with the supplied reagents for 17 cycles. Pooled libraries were sequenced on an Illumina HiSeq 2500. Sequencing was run for 50 cycles, with read length of 50 bp (single reads). Illumina HiSeq 2500 gds 302338948 GSM2338948 GEO Accession GSM2338948 SRX2228635 GSM2338949 SRP090981 PRJNA347285 SRS1732826 SAMN05878585 RNA-Seq TRANSCRIPTOMIC cDNA Briefly, RNA was obtained using the Ambion RNAqeous kit (LifeTechnologies), with a pretreatment using 250 μl lysozyme (50 mg/ml final; Sigma) and 125 μl mutanolysin (1000 units/ml; Sigma), at 37˚C for 10 min. Total RNA was immediately subjected to DNase treatment with the Turbo DNase free (Ambion) using 3 μl of DNase I for 1 hour at 37º C. RNA integrity was checked in a Bioanalyzer using an Agilent RNA Nano Chip, with a minimal RIN (RNA Integrity Number) of 7. Genomic DNA contamination was evaluated by qPCR and universal bacterial primers Uni334F and Uni514R53. Ribosomal RNA depletion was achieved using the Ribo-Zero magnetic kit Bacteria (Epicentre, Madison WA). Manufacturer instructions were followed (using 28 or 26 μl of RNA depending on the concentration). mRNA was purified with the Qiagen RNeasy Minelute Cleanup kit, following the instructions presented in the Ribo-Zero protocol for this part. RNA was eluted in 13 µl. One μl of the RNA was checked for removal of 16S and 23S rRNA peaks using the Qubit HS RNA Assay (Agilent). Chromatograms were manually inspected. Messenger RNA was finally converted to cDNA. For first strand cDNA synthesis, the Superscript II Reverse Transcriptase was used (Invitrogen) and second cDNA strand was synthesized using the NEBNext mRNA Second Strand Synthesis Module (New England Biolabs, Ipswich, MA). Then, the MinElute Reaction Cleanup Kit (Qiagen, Valencia CA) was used for cleaning up the DNA. cDNA was quantified using the Qubit High Sensitivity DNA kit (Life Technologies), and fragmented in a Bioruptor (Diagenode). An average fragment length of 300-500 bp was desired for next steps. Sequencing libraries were prepared using the BiooScientific NEXTflex Chip Seq Kit (Bioo Scientific, Austin TX). This kit is Illumina compatible. Ten ng of fragmented cDNA were used. In the manufacturer protocol, option 3 was followed entirely, with the goal to select fragments between 300 and 400 bp in a gel-free protocol. Size selection and clean-up steps were achieved using the Agencourt Ampure XP beads (Beckman Coulter, Brea CA), and a Magnetic Stand-96 (LifeTechnologies). All temperature-sensitive reactions were carried out in a preheated thermocycler. Adapters used (NEXTflex™ ChIP-Seq Barcodes, Bioo Scientific) contained 6-bp indexes for multiplexing. At the last step, ligation products were amplified by PCR with the supplied reagents for 17 cycles. Pooled libraries were sequenced on an Illumina HiSeq 2500. Sequencing was run for 50 cycles, with read length of 50 bp (single reads). Illumina HiSeq 2500 gds 302338949 GSM2338949 GEO Accession GSM2338949 SRX2228636 GSM2338950 SRP090981 PRJNA347285 SRS1732827 SAMN05878584 RNA-Seq TRANSCRIPTOMIC cDNA Briefly, RNA was obtained using the Ambion RNAqeous kit (LifeTechnologies), with a pretreatment using 250 μl lysozyme (50 mg/ml final; Sigma) and 125 μl mutanolysin (1000 units/ml; Sigma), at 37˚C for 10 min. Total RNA was immediately subjected to DNase treatment with the Turbo DNase free (Ambion) using 3 μl of DNase I for 1 hour at 37º C. RNA integrity was checked in a Bioanalyzer using an Agilent RNA Nano Chip, with a minimal RIN (RNA Integrity Number) of 7. Genomic DNA contamination was evaluated by qPCR and universal bacterial primers Uni334F and Uni514R53. Ribosomal RNA depletion was achieved using the Ribo-Zero magnetic kit Bacteria (Epicentre, Madison WA). Manufacturer instructions were followed (using 28 or 26 μl of RNA depending on the concentration). mRNA was purified with the Qiagen RNeasy Minelute Cleanup kit, following the instructions presented in the Ribo-Zero protocol for this part. RNA was eluted in 13 µl. One μl of the RNA was checked for removal of 16S and 23S rRNA peaks using the Qubit HS RNA Assay (Agilent). Chromatograms were manually inspected. Messenger RNA was finally converted to cDNA. For first strand cDNA synthesis, the Superscript II Reverse Transcriptase was used (Invitrogen) and second cDNA strand was synthesized using the NEBNext mRNA Second Strand Synthesis Module (New England Biolabs, Ipswich, MA). Then, the MinElute Reaction Cleanup Kit (Qiagen, Valencia CA) was used for cleaning up the DNA. cDNA was quantified using the Qubit High Sensitivity DNA kit (Life Technologies), and fragmented in a Bioruptor (Diagenode). An average fragment length of 300-500 bp was desired for next steps. Sequencing libraries were prepared using the BiooScientific NEXTflex Chip Seq Kit (Bioo Scientific, Austin TX). This kit is Illumina compatible. Ten ng of fragmented cDNA were used. In the manufacturer protocol, option 3 was followed entirely, with the goal to select fragments between 300 and 400 bp in a gel-free protocol. Size selection and clean-up steps were achieved using the Agencourt Ampure XP beads (Beckman Coulter, Brea CA), and a Magnetic Stand-96 (LifeTechnologies). All temperature-sensitive reactions were carried out in a preheated thermocycler. Adapters used (NEXTflex™ ChIP-Seq Barcodes, Bioo Scientific) contained 6-bp indexes for multiplexing. At the last step, ligation products were amplified by PCR with the supplied reagents for 17 cycles. Pooled libraries were sequenced on an Illumina HiSeq 2500. Sequencing was run for 50 cycles, with read length of 50 bp (single reads). Illumina HiSeq 2500 gds 302338950 GSM2338950 GEO Accession GSM2338950 SRX2228637 GSM2338951 SRP090981 PRJNA347285 SRS1732828 SAMN05878583 RNA-Seq TRANSCRIPTOMIC cDNA Briefly, RNA was obtained using the Ambion RNAqeous kit (LifeTechnologies), with a pretreatment using 250 μl lysozyme (50 mg/ml final; Sigma) and 125 μl mutanolysin (1000 units/ml; Sigma), at 37˚C for 10 min. Total RNA was immediately subjected to DNase treatment with the Turbo DNase free (Ambion) using 3 μl of DNase I for 1 hour at 37º C. RNA integrity was checked in a Bioanalyzer using an Agilent RNA Nano Chip, with a minimal RIN (RNA Integrity Number) of 7. Genomic DNA contamination was evaluated by qPCR and universal bacterial primers Uni334F and Uni514R53. Ribosomal RNA depletion was achieved using the Ribo-Zero magnetic kit Bacteria (Epicentre, Madison WA). Manufacturer instructions were followed (using 28 or 26 μl of RNA depending on the concentration). mRNA was purified with the Qiagen RNeasy Minelute Cleanup kit, following the instructions presented in the Ribo-Zero protocol for this part. RNA was eluted in 13 µl. One μl of the RNA was checked for removal of 16S and 23S rRNA peaks using the Qubit HS RNA Assay (Agilent). Chromatograms were manually inspected. Messenger RNA was finally converted to cDNA. For first strand cDNA synthesis, the Superscript II Reverse Transcriptase was used (Invitrogen) and second cDNA strand was synthesized using the NEBNext mRNA Second Strand Synthesis Module (New England Biolabs, Ipswich, MA). Then, the MinElute Reaction Cleanup Kit (Qiagen, Valencia CA) was used for cleaning up the DNA. cDNA was quantified using the Qubit High Sensitivity DNA kit (Life Technologies), and fragmented in a Bioruptor (Diagenode). An average fragment length of 300-500 bp was desired for next steps. Sequencing libraries were prepared using the BiooScientific NEXTflex Chip Seq Kit (Bioo Scientific, Austin TX). This kit is Illumina compatible. Ten ng of fragmented cDNA were used. In the manufacturer protocol, option 3 was followed entirely, with the goal to select fragments between 300 and 400 bp in a gel-free protocol. Size selection and clean-up steps were achieved using the Agencourt Ampure XP beads (Beckman Coulter, Brea CA), and a Magnetic Stand-96 (LifeTechnologies). All temperature-sensitive reactions were carried out in a preheated thermocycler. Adapters used (NEXTflex™ ChIP-Seq Barcodes, Bioo Scientific) contained 6-bp indexes for multiplexing. At the last step, ligation products were amplified by PCR with the supplied reagents for 17 cycles. Pooled libraries were sequenced on an Illumina HiSeq 2500. Sequencing was run for 50 cycles, with read length of 50 bp (single reads). Illumina HiSeq 2500 gds 302338951 GSM2338951 GEO Accession GSM2338951 SRX2228638 GSM2338952 SRP090981 PRJNA347285 SRS1732829 SAMN05878582 RNA-Seq TRANSCRIPTOMIC cDNA Briefly, RNA was obtained using the Ambion RNAqeous kit (LifeTechnologies), with a pretreatment using 250 μl lysozyme (50 mg/ml final; Sigma) and 125 μl mutanolysin (1000 units/ml; Sigma), at 37˚C for 10 min. Total RNA was immediately subjected to DNase treatment with the Turbo DNase free (Ambion) using 3 μl of DNase I for 1 hour at 37º C. RNA integrity was checked in a Bioanalyzer using an Agilent RNA Nano Chip, with a minimal RIN (RNA Integrity Number) of 7. Genomic DNA contamination was evaluated by qPCR and universal bacterial primers Uni334F and Uni514R53. Ribosomal RNA depletion was achieved using the Ribo-Zero magnetic kit Bacteria (Epicentre, Madison WA). Manufacturer instructions were followed (using 28 or 26 μl of RNA depending on the concentration). mRNA was purified with the Qiagen RNeasy Minelute Cleanup kit, following the instructions presented in the Ribo-Zero protocol for this part. RNA was eluted in 13 µl. One μl of the RNA was checked for removal of 16S and 23S rRNA peaks using the Qubit HS RNA Assay (Agilent). Chromatograms were manually inspected. Messenger RNA was finally converted to cDNA. For first strand cDNA synthesis, the Superscript II Reverse Transcriptase was used (Invitrogen) and second cDNA strand was synthesized using the NEBNext mRNA Second Strand Synthesis Module (New England Biolabs, Ipswich, MA). Then, the MinElute Reaction Cleanup Kit (Qiagen, Valencia CA) was used for cleaning up the DNA. cDNA was quantified using the Qubit High Sensitivity DNA kit (Life Technologies), and fragmented in a Bioruptor (Diagenode). An average fragment length of 300-500 bp was desired for next steps. Sequencing libraries were prepared using the BiooScientific NEXTflex Chip Seq Kit (Bioo Scientific, Austin TX). This kit is Illumina compatible. Ten ng of fragmented cDNA were used. In the manufacturer protocol, option 3 was followed entirely, with the goal to select fragments between 300 and 400 bp in a gel-free protocol. Size selection and clean-up steps were achieved using the Agencourt Ampure XP beads (Beckman Coulter, Brea CA), and a Magnetic Stand-96 (LifeTechnologies). All temperature-sensitive reactions were carried out in a preheated thermocycler. Adapters used (NEXTflex™ ChIP-Seq Barcodes, Bioo Scientific) contained 6-bp indexes for multiplexing. At the last step, ligation products were amplified by PCR with the supplied reagents for 17 cycles. Pooled libraries were sequenced on an Illumina HiSeq 2500. Sequencing was run for 50 cycles, with read length of 50 bp (single reads). Illumina HiSeq 2500 gds 302338952 GSM2338952 GEO Accession GSM2338952 SRX2228639 GSM2338953 SRP090981 PRJNA347285 SRS1732830 SAMN05878581 RNA-Seq TRANSCRIPTOMIC cDNA Briefly, RNA was obtained using the Ambion RNAqeous kit (LifeTechnologies), with a pretreatment using 250 μl lysozyme (50 mg/ml final; Sigma) and 125 μl mutanolysin (1000 units/ml; Sigma), at 37˚C for 10 min. Total RNA was immediately subjected to DNase treatment with the Turbo DNase free (Ambion) using 3 μl of DNase I for 1 hour at 37º C. RNA integrity was checked in a Bioanalyzer using an Agilent RNA Nano Chip, with a minimal RIN (RNA Integrity Number) of 7. Genomic DNA contamination was evaluated by qPCR and universal bacterial primers Uni334F and Uni514R53. Ribosomal RNA depletion was achieved using the Ribo-Zero magnetic kit Bacteria (Epicentre, Madison WA). Manufacturer instructions were followed (using 28 or 26 μl of RNA depending on the concentration). mRNA was purified with the Qiagen RNeasy Minelute Cleanup kit, following the instructions presented in the Ribo-Zero protocol for this part. RNA was eluted in 13 µl. One μl of the RNA was checked for removal of 16S and 23S rRNA peaks using the Qubit HS RNA Assay (Agilent). Chromatograms were manually inspected. Messenger RNA was finally converted to cDNA. For first strand cDNA synthesis, the Superscript II Reverse Transcriptase was used (Invitrogen) and second cDNA strand was synthesized using the NEBNext mRNA Second Strand Synthesis Module (New England Biolabs, Ipswich, MA). Then, the MinElute Reaction Cleanup Kit (Qiagen, Valencia CA) was used for cleaning up the DNA. cDNA was quantified using the Qubit High Sensitivity DNA kit (Life Technologies), and fragmented in a Bioruptor (Diagenode). An average fragment length of 300-500 bp was desired for next steps. Sequencing libraries were prepared using the BiooScientific NEXTflex Chip Seq Kit (Bioo Scientific, Austin TX). This kit is Illumina compatible. Ten ng of fragmented cDNA were used. In the manufacturer protocol, option 3 was followed entirely, with the goal to select fragments between 300 and 400 bp in a gel-free protocol. Size selection and clean-up steps were achieved using the Agencourt Ampure XP beads (Beckman Coulter, Brea CA), and a Magnetic Stand-96 (LifeTechnologies). All temperature-sensitive reactions were carried out in a preheated thermocycler. Adapters used (NEXTflex™ ChIP-Seq Barcodes, Bioo Scientific) contained 6-bp indexes for multiplexing. At the last step, ligation products were amplified by PCR with the supplied reagents for 17 cycles. Pooled libraries were sequenced on an Illumina HiSeq 2500. Sequencing was run for 50 cycles, with read length of 50 bp (single reads). Illumina HiSeq 2500 gds 302338953 GSM2338953 GEO Accession GSM2338953 SRX2228640 GSM2338954 SRP090981 PRJNA347285 SRS1732832 SAMN05878580 RNA-Seq TRANSCRIPTOMIC cDNA Briefly, RNA was obtained using the Ambion RNAqeous kit (LifeTechnologies), with a pretreatment using 250 μl lysozyme (50 mg/ml final; Sigma) and 125 μl mutanolysin (1000 units/ml; Sigma), at 37˚C for 10 min. Total RNA was immediately subjected to DNase treatment with the Turbo DNase free (Ambion) using 3 μl of DNase I for 1 hour at 37º C. RNA integrity was checked in a Bioanalyzer using an Agilent RNA Nano Chip, with a minimal RIN (RNA Integrity Number) of 7. Genomic DNA contamination was evaluated by qPCR and universal bacterial primers Uni334F and Uni514R53. Ribosomal RNA depletion was achieved using the Ribo-Zero magnetic kit Bacteria (Epicentre, Madison WA). Manufacturer instructions were followed (using 28 or 26 μl of RNA depending on the concentration). mRNA was purified with the Qiagen RNeasy Minelute Cleanup kit, following the instructions presented in the Ribo-Zero protocol for this part. RNA was eluted in 13 µl. One μl of the RNA was checked for removal of 16S and 23S rRNA peaks using the Qubit HS RNA Assay (Agilent). Chromatograms were manually inspected. Messenger RNA was finally converted to cDNA. For first strand cDNA synthesis, the Superscript II Reverse Transcriptase was used (Invitrogen) and second cDNA strand was synthesized using the NEBNext mRNA Second Strand Synthesis Module (New England Biolabs, Ipswich, MA). Then, the MinElute Reaction Cleanup Kit (Qiagen, Valencia CA) was used for cleaning up the DNA. cDNA was quantified using the Qubit High Sensitivity DNA kit (Life Technologies), and fragmented in a Bioruptor (Diagenode). An average fragment length of 300-500 bp was desired for next steps. Sequencing libraries were prepared using the BiooScientific NEXTflex Chip Seq Kit (Bioo Scientific, Austin TX). This kit is Illumina compatible. Ten ng of fragmented cDNA were used. In the manufacturer protocol, option 3 was followed entirely, with the goal to select fragments between 300 and 400 bp in a gel-free protocol. Size selection and clean-up steps were achieved using the Agencourt Ampure XP beads (Beckman Coulter, Brea CA), and a Magnetic Stand-96 (LifeTechnologies). All temperature-sensitive reactions were carried out in a preheated thermocycler. Adapters used (NEXTflex™ ChIP-Seq Barcodes, Bioo Scientific) contained 6-bp indexes for multiplexing. At the last step, ligation products were amplified by PCR with the supplied reagents for 17 cycles. Pooled libraries were sequenced on an Illumina HiSeq 2500. Sequencing was run for 50 cycles, with read length of 50 bp (single reads). Illumina HiSeq 2500 gds 302338954 GSM2338954 GEO Accession GSM2338954 SRX2228641 GSM2338955 SRP090981 PRJNA347285 SRS1732831 SAMN05878579 RNA-Seq TRANSCRIPTOMIC cDNA Briefly, RNA was obtained using the Ambion RNAqeous kit (LifeTechnologies), with a pretreatment using 250 μl lysozyme (50 mg/ml final; Sigma) and 125 μl mutanolysin (1000 units/ml; Sigma), at 37˚C for 10 min. Total RNA was immediately subjected to DNase treatment with the Turbo DNase free (Ambion) using 3 μl of DNase I for 1 hour at 37º C. RNA integrity was checked in a Bioanalyzer using an Agilent RNA Nano Chip, with a minimal RIN (RNA Integrity Number) of 7. Genomic DNA contamination was evaluated by qPCR and universal bacterial primers Uni334F and Uni514R53. Ribosomal RNA depletion was achieved using the Ribo-Zero magnetic kit Bacteria (Epicentre, Madison WA). Manufacturer instructions were followed (using 28 or 26 μl of RNA depending on the concentration). mRNA was purified with the Qiagen RNeasy Minelute Cleanup kit, following the instructions presented in the Ribo-Zero protocol for this part. RNA was eluted in 13 µl. One μl of the RNA was checked for removal of 16S and 23S rRNA peaks using the Qubit HS RNA Assay (Agilent). Chromatograms were manually inspected. Messenger RNA was finally converted to cDNA. For first strand cDNA synthesis, the Superscript II Reverse Transcriptase was used (Invitrogen) and second cDNA strand was synthesized using the NEBNext mRNA Second Strand Synthesis Module (New England Biolabs, Ipswich, MA). Then, the MinElute Reaction Cleanup Kit (Qiagen, Valencia CA) was used for cleaning up the DNA. cDNA was quantified using the Qubit High Sensitivity DNA kit (Life Technologies), and fragmented in a Bioruptor (Diagenode). An average fragment length of 300-500 bp was desired for next steps. Sequencing libraries were prepared using the BiooScientific NEXTflex Chip Seq Kit (Bioo Scientific, Austin TX). This kit is Illumina compatible. Ten ng of fragmented cDNA were used. In the manufacturer protocol, option 3 was followed entirely, with the goal to select fragments between 300 and 400 bp in a gel-free protocol. Size selection and clean-up steps were achieved using the Agencourt Ampure XP beads (Beckman Coulter, Brea CA), and a Magnetic Stand-96 (LifeTechnologies). All temperature-sensitive reactions were carried out in a preheated thermocycler. Adapters used (NEXTflex™ ChIP-Seq Barcodes, Bioo Scientific) contained 6-bp indexes for multiplexing. At the last step, ligation products were amplified by PCR with the supplied reagents for 17 cycles. Pooled libraries were sequenced on an Illumina HiSeq 2500. Sequencing was run for 50 cycles, with read length of 50 bp (single reads). Illumina HiSeq 2500 gds 302338955 GSM2338955 GEO Accession GSM2338955 SRX2228642 GSM2338956 SRP090981 PRJNA347285 SRS1732833 SAMN05878578 RNA-Seq TRANSCRIPTOMIC cDNA Briefly, RNA was obtained using the Ambion RNAqeous kit (LifeTechnologies), with a pretreatment using 250 μl lysozyme (50 mg/ml final; Sigma) and 125 μl mutanolysin (1000 units/ml; Sigma), at 37˚C for 10 min. Total RNA was immediately subjected to DNase treatment with the Turbo DNase free (Ambion) using 3 μl of DNase I for 1 hour at 37º C. RNA integrity was checked in a Bioanalyzer using an Agilent RNA Nano Chip, with a minimal RIN (RNA Integrity Number) of 7. Genomic DNA contamination was evaluated by qPCR and universal bacterial primers Uni334F and Uni514R53. Ribosomal RNA depletion was achieved using the Ribo-Zero magnetic kit Bacteria (Epicentre, Madison WA). Manufacturer instructions were followed (using 28 or 26 μl of RNA depending on the concentration). mRNA was purified with the Qiagen RNeasy Minelute Cleanup kit, following the instructions presented in the Ribo-Zero protocol for this part. RNA was eluted in 13 µl. One μl of the RNA was checked for removal of 16S and 23S rRNA peaks using the Qubit HS RNA Assay (Agilent). Chromatograms were manually inspected. Messenger RNA was finally converted to cDNA. For first strand cDNA synthesis, the Superscript II Reverse Transcriptase was used (Invitrogen) and second cDNA strand was synthesized using the NEBNext mRNA Second Strand Synthesis Module (New England Biolabs, Ipswich, MA). Then, the MinElute Reaction Cleanup Kit (Qiagen, Valencia CA) was used for cleaning up the DNA. cDNA was quantified using the Qubit High Sensitivity DNA kit (Life Technologies), and fragmented in a Bioruptor (Diagenode). An average fragment length of 300-500 bp was desired for next steps. Sequencing libraries were prepared using the BiooScientific NEXTflex Chip Seq Kit (Bioo Scientific, Austin TX). This kit is Illumina compatible. Ten ng of fragmented cDNA were used. In the manufacturer protocol, option 3 was followed entirely, with the goal to select fragments between 300 and 400 bp in a gel-free protocol. Size selection and clean-up steps were achieved using the Agencourt Ampure XP beads (Beckman Coulter, Brea CA), and a Magnetic Stand-96 (LifeTechnologies). All temperature-sensitive reactions were carried out in a preheated thermocycler. Adapters used (NEXTflex™ ChIP-Seq Barcodes, Bioo Scientific) contained 6-bp indexes for multiplexing. At the last step, ligation products were amplified by PCR with the supplied reagents for 17 cycles. Pooled libraries were sequenced on an Illumina HiSeq 2500. Sequencing was run for 50 cycles, with read length of 50 bp (single reads). Illumina HiSeq 2500 gds 302338956 GSM2338956 GEO Accession GSM2338956 SRX2228643 GSM2338957 SRP090981 PRJNA347285 SRS1732834 SAMN05878577 RNA-Seq TRANSCRIPTOMIC cDNA Briefly, RNA was obtained using the Ambion RNAqeous kit (LifeTechnologies), with a pretreatment using 250 μl lysozyme (50 mg/ml final; Sigma) and 125 μl mutanolysin (1000 units/ml; Sigma), at 37˚C for 10 min. Total RNA was immediately subjected to DNase treatment with the Turbo DNase free (Ambion) using 3 μl of DNase I for 1 hour at 37º C. RNA integrity was checked in a Bioanalyzer using an Agilent RNA Nano Chip, with a minimal RIN (RNA Integrity Number) of 7. Genomic DNA contamination was evaluated by qPCR and universal bacterial primers Uni334F and Uni514R53. Ribosomal RNA depletion was achieved using the Ribo-Zero magnetic kit Bacteria (Epicentre, Madison WA). Manufacturer instructions were followed (using 28 or 26 μl of RNA depending on the concentration). mRNA was purified with the Qiagen RNeasy Minelute Cleanup kit, following the instructions presented in the Ribo-Zero protocol for this part. RNA was eluted in 13 µl. One μl of the RNA was checked for removal of 16S and 23S rRNA peaks using the Qubit HS RNA Assay (Agilent). Chromatograms were manually inspected. Messenger RNA was finally converted to cDNA. For first strand cDNA synthesis, the Superscript II Reverse Transcriptase was used (Invitrogen) and second cDNA strand was synthesized using the NEBNext mRNA Second Strand Synthesis Module (New England Biolabs, Ipswich, MA). Then, the MinElute Reaction Cleanup Kit (Qiagen, Valencia CA) was used for cleaning up the DNA. cDNA was quantified using the Qubit High Sensitivity DNA kit (Life Technologies), and fragmented in a Bioruptor (Diagenode). An average fragment length of 300-500 bp was desired for next steps. Sequencing libraries were prepared using the BiooScientific NEXTflex Chip Seq Kit (Bioo Scientific, Austin TX). This kit is Illumina compatible. Ten ng of fragmented cDNA were used. In the manufacturer protocol, option 3 was followed entirely, with the goal to select fragments between 300 and 400 bp in a gel-free protocol. Size selection and clean-up steps were achieved using the Agencourt Ampure XP beads (Beckman Coulter, Brea CA), and a Magnetic Stand-96 (LifeTechnologies). All temperature-sensitive reactions were carried out in a preheated thermocycler. Adapters used (NEXTflex™ ChIP-Seq Barcodes, Bioo Scientific) contained 6-bp indexes for multiplexing. At the last step, ligation products were amplified by PCR with the supplied reagents for 17 cycles. Pooled libraries were sequenced on an Illumina HiSeq 2500. Sequencing was run for 50 cycles, with read length of 50 bp (single reads). Illumina HiSeq 2500 gds 302338957 GSM2338957 GEO Accession GSM2338957 SRX2228644 GSM2338958 SRP090981 PRJNA347285 SRS1732835 SAMN05878576 RNA-Seq TRANSCRIPTOMIC cDNA Briefly, RNA was obtained using the Ambion RNAqeous kit (LifeTechnologies), with a pretreatment using 250 μl lysozyme (50 mg/ml final; Sigma) and 125 μl mutanolysin (1000 units/ml; Sigma), at 37˚C for 10 min. Total RNA was immediately subjected to DNase treatment with the Turbo DNase free (Ambion) using 3 μl of DNase I for 1 hour at 37º C. RNA integrity was checked in a Bioanalyzer using an Agilent RNA Nano Chip, with a minimal RIN (RNA Integrity Number) of 7. Genomic DNA contamination was evaluated by qPCR and universal bacterial primers Uni334F and Uni514R53. Ribosomal RNA depletion was achieved using the Ribo-Zero magnetic kit Bacteria (Epicentre, Madison WA). Manufacturer instructions were followed (using 28 or 26 μl of RNA depending on the concentration). mRNA was purified with the Qiagen RNeasy Minelute Cleanup kit, following the instructions presented in the Ribo-Zero protocol for this part. RNA was eluted in 13 µl. One μl of the RNA was checked for removal of 16S and 23S rRNA peaks using the Qubit HS RNA Assay (Agilent). Chromatograms were manually inspected. Messenger RNA was finally converted to cDNA. For first strand cDNA synthesis, the Superscript II Reverse Transcriptase was used (Invitrogen) and second cDNA strand was synthesized using the NEBNext mRNA Second Strand Synthesis Module (New England Biolabs, Ipswich, MA). Then, the MinElute Reaction Cleanup Kit (Qiagen, Valencia CA) was used for cleaning up the DNA. cDNA was quantified using the Qubit High Sensitivity DNA kit (Life Technologies), and fragmented in a Bioruptor (Diagenode). An average fragment length of 300-500 bp was desired for next steps. Sequencing libraries were prepared using the BiooScientific NEXTflex Chip Seq Kit (Bioo Scientific, Austin TX). This kit is Illumina compatible. Ten ng of fragmented cDNA were used. In the manufacturer protocol, option 3 was followed entirely, with the goal to select fragments between 300 and 400 bp in a gel-free protocol. Size selection and clean-up steps were achieved using the Agencourt Ampure XP beads (Beckman Coulter, Brea CA), and a Magnetic Stand-96 (LifeTechnologies). All temperature-sensitive reactions were carried out in a preheated thermocycler. Adapters used (NEXTflex™ ChIP-Seq Barcodes, Bioo Scientific) contained 6-bp indexes for multiplexing. At the last step, ligation products were amplified by PCR with the supplied reagents for 17 cycles. Pooled libraries were sequenced on an Illumina HiSeq 2500. Sequencing was run for 50 cycles, with read length of 50 bp (single reads). Illumina HiSeq 2500 gds 302338958 GSM2338958 GEO Accession GSM2338958