ERS10393959 SAMEA12788610 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788610 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA14358-1b_plusAHTc broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan growth condition Lysogeny Broth (LB) with anhydrotetracycline isolate not applicable organism part whole organism phenotype SPI-1 inactivation; Ptet activation sample name E-MTAB-11419:MA14358-1b_plusAHTc strain MA14358 serovar Typhimurium sub_species enterica ERS10393969 SAMEA12788620 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788620 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA14358-3a_plusARA_plusAHTc broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan growth condition Lysogeny Broth (LB) with arabinose and anhydrotetracycline isolate not applicable organism part whole organism phenotype SPI-1 inactivation; NusG depletion; Ptet activation sample name E-MTAB-11419:MA14358-3a_plusARA_plusAHTc strain MA14358 serovar Typhimurium sub_species enterica ERS10393975 SAMEA12788626 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788626 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA14358-4a_plusAHTc broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan growth condition Lysogeny Broth (LB) with anhydrotetracycline isolate not applicable organism part whole organism phenotype SPI-1 inactivation; Ptet activation sample name E-MTAB-11419:MA14358-4a_plusAHTc strain MA14358 serovar Typhimurium sub_species enterica ERS10393970 SAMEA12788621 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788621 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA14358-3a_untreated broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan growth condition Lysogeny Broth (LB) isolate not applicable organism part whole organism phenotype SPI-1 inactivation sample name E-MTAB-11419:MA14358-3a_untreated strain MA14358 serovar Typhimurium sub_species enterica ERS10393961 SAMEA12788612 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788612 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA14358-1b_plusARA_plusAHTc broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan growth condition Lysogeny Broth (LB) with arabinose and anhydrotetracycline isolate not applicable organism part whole organism phenotype SPI-1 inactivation; NusG depletion; Ptet activation sample name E-MTAB-11419:MA14358-1b_plusARA_plusAHTc strain MA14358 serovar Typhimurium sub_species enterica ERS10393978 SAMEA12788629 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788629 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA14358-4a_untreated broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan growth condition Lysogeny Broth (LB) isolate not applicable organism part whole organism phenotype SPI-1 inactivation sample name E-MTAB-11419:MA14358-4a_untreated strain MA14358 serovar Typhimurium sub_species enterica ERS10393962 SAMEA12788613 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788613 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA14358-1b_untreated broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan growth condition Lysogeny Broth (LB) isolate not applicable organism part whole organism phenotype SPI-1 inactivation sample name E-MTAB-11419:MA14358-1b_untreated strain MA14358 serovar Typhimurium sub_species enterica ERS10393944 SAMEA12788595 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788595 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA12996-1a_untreated broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA growth condition Lysogeny Broth (LB) isolate not applicable organism part whole organism phenotype wild type sample name E-MTAB-11419:MA12996-1a_untreated strain MA12996 serovar Typhimurium sub_species enterica ERS10393968 SAMEA12788619 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). phenotype SPI-1 inactivation; NusG depletion strain MA14358 isolate not applicable ENA-FIRST-PUBLIC 2022-07-05T12:07:22Z organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ENA-LAST-UPDATE 2022-07-05T12:07:22Z growth condition Lysogeny Broth (LB) with arabinose scientific_name Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism part whole organism genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 ERS10393948 SAMEA12788599 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). phenotype wild type strain MA12996 isolate not applicable ENA-FIRST-PUBLIC 2022-07-05T12:07:22Z organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ENA-LAST-UPDATE 2022-07-05T12:07:22Z growth condition Lysogeny Broth (LB) scientific_name Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism part whole organism genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 ERS10393965 SAMEA12788616 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). phenotype SPI-1 inactivation; NusG depletion; Ptet activation strain MA14358 isolate not applicable ENA-FIRST-PUBLIC 2022-07-05T12:07:22Z organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ENA-LAST-UPDATE 2022-07-05T12:07:22Z growth condition Lysogeny Broth (LB) with arabinose and anhydrotetracycline scientific_name Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism part whole organism genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 ERS10393971 SAMEA12788622 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). phenotype SPI-1 inactivation; Ptet activation strain MA14358 isolate not applicable ENA-FIRST-PUBLIC 2022-07-05T12:07:22Z organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ENA-LAST-UPDATE 2022-07-05T12:07:22Z growth condition Lysogeny Broth (LB) with anhydrotetracycline scientific_name Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism part whole organism genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 ERS10393943 SAMEA12788594 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). phenotype NusG depletion strain MA12996 isolate not applicable ENA-FIRST-PUBLIC 2022-07-05T12:07:22Z organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ENA-LAST-UPDATE 2022-07-05T12:07:22Z growth condition Lysogeny Broth (LB) with arabinose scientific_name Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism part whole organism genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 ERS10393982 SAMEA12788633 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). phenotype SPI-1 inactivation strain MA14358 isolate not applicable ENA-FIRST-PUBLIC 2022-07-05T12:07:22Z organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ENA-LAST-UPDATE 2022-07-05T12:07:22Z growth condition Lysogeny Broth (LB) scientific_name Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism part whole organism genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 ERS10393972 SAMEA12788623 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). phenotype SPI-1 inactivation; NusG depletion strain MA14358 isolate not applicable ENA-FIRST-PUBLIC 2022-07-05T12:07:22Z organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ENA-LAST-UPDATE 2022-07-05T12:07:22Z growth condition Lysogeny Broth (LB) with arabinose scientific_name Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism part whole organism genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 ERS10393977 SAMEA12788628 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788628 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA14358-4a_plusARA_plusAHTc broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan growth condition Lysogeny Broth (LB) with arabinose and anhydrotetracycline isolate not applicable organism part whole organism phenotype SPI-1 inactivation; NusG depletion; Ptet activation sample name E-MTAB-11419:MA14358-4a_plusARA_plusAHTc strain MA14358 serovar Typhimurium sub_species enterica ERS10393956 SAMEA12788607 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788607 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA14358-1a_plusARA broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan growth condition Lysogeny Broth (LB) with arabinose isolate not applicable organism part whole organism phenotype SPI-1 inactivation; NusG depletion sample name E-MTAB-11419:MA14358-1a_plusARA strain MA14358 serovar Typhimurium sub_species enterica ERS10393973 SAMEA12788624 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788624 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA14358-3b_plusARA_plusAHTc broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan growth condition Lysogeny Broth (LB) with arabinose and anhydrotetracycline isolate not applicable organism part whole organism phenotype SPI-1 inactivation; NusG depletion; Ptet activation sample name E-MTAB-11419:MA14358-3b_plusARA_plusAHTc strain MA14358 serovar Typhimurium sub_species enterica ERS10393974 SAMEA12788625 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788625 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA14358-3b_untreated broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan growth condition Lysogeny Broth (LB) isolate not applicable organism part whole organism phenotype SPI-1 inactivation sample name E-MTAB-11419:MA14358-3b_untreated strain MA14358 serovar Typhimurium sub_species enterica ERS10393954 SAMEA12788605 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). phenotype wild type strain MA14302 isolate not applicable ENA-FIRST-PUBLIC 2022-07-05T12:07:22Z organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ENA-LAST-UPDATE 2022-07-05T12:07:22Z growth condition Lysogeny Broth (LB) scientific_name Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism part whole organism genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry hilA::gfpSF ∆K28-kan ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 ERS10393958 SAMEA12788609 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788609 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA14358-1a_untreated broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan growth condition Lysogeny Broth (LB) isolate not applicable organism part whole organism phenotype SPI-1 inactivation sample name E-MTAB-11419:MA14358-1a_untreated strain MA14358 serovar Typhimurium sub_species enterica ERS10393945 SAMEA12788596 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788596 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA12996-1b_plusARA broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA growth condition Lysogeny Broth (LB) with arabinose isolate not applicable organism part whole organism phenotype NusG depletion sample name E-MTAB-11419:MA12996-1b_plusARA strain MA12996 serovar Typhimurium sub_species enterica ERS10393946 SAMEA12788597 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788597 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA12996-1b_untreated broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA growth condition Lysogeny Broth (LB) isolate not applicable organism part whole organism phenotype wild type sample name E-MTAB-11419:MA12996-1b_untreated strain MA12996 serovar Typhimurium sub_species enterica ERS10393955 SAMEA12788606 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). phenotype SPI-1 inactivation; Ptet activation strain MA14358 isolate not applicable ENA-FIRST-PUBLIC 2022-07-05T12:07:22Z organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ENA-LAST-UPDATE 2022-07-05T12:07:22Z growth condition Lysogeny Broth (LB) with anhydrotetracycline scientific_name Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism part whole organism genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 ERS10393947 SAMEA12788598 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). phenotype NusG depletion strain MA12996 isolate not applicable ENA-FIRST-PUBLIC 2022-07-05T12:07:22Z organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ENA-LAST-UPDATE 2022-07-05T12:07:22Z growth condition Lysogeny Broth (LB) with arabinose scientific_name Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism part whole organism genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 ERS10393967 SAMEA12788618 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). phenotype SPI-1 inactivation; Ptet activation strain MA14358 isolate not applicable ENA-FIRST-PUBLIC 2022-07-05T12:07:22Z organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ENA-LAST-UPDATE 2022-07-05T12:07:22Z growth condition Lysogeny Broth (LB) with anhydrotetracycline scientific_name Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism part whole organism genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 ERS10393949 SAMEA12788600 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788600 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA12996-2b_plusARA broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA growth condition Lysogeny Broth (LB) with arabinose isolate not applicable organism part whole organism phenotype NusG depletion sample name E-MTAB-11419:MA12996-2b_plusARA strain MA12996 serovar Typhimurium sub_species enterica ERS10393979 SAMEA12788630 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788630 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA14358-4b_plusAHTc broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan growth condition Lysogeny Broth (LB) with anhydrotetracycline isolate not applicable organism part whole organism phenotype SPI-1 inactivation; Ptet activation sample name E-MTAB-11419:MA14358-4b_plusAHTc strain MA14358 serovar Typhimurium sub_species enterica ERS10393981 SAMEA12788632 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788632 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA14358-4b_plusARA_plusAHTc broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan growth condition Lysogeny Broth (LB) with arabinose and anhydrotetracycline isolate not applicable organism part whole organism phenotype SPI-1 inactivation; NusG depletion; Ptet activation sample name E-MTAB-11419:MA14358-4b_plusARA_plusAHTc strain MA14358 serovar Typhimurium sub_species enterica ERS10393957 SAMEA12788608 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788608 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA14358-1a_plusARA_plusAHTc broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan growth condition Lysogeny Broth (LB) with arabinose and anhydrotetracycline isolate not applicable organism part whole organism phenotype SPI-1 inactivation; NusG depletion; Ptet activation sample name E-MTAB-11419:MA14358-1a_plusARA_plusAHTc strain MA14358 serovar Typhimurium sub_species enterica ERS10393963 SAMEA12788614 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788614 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA14358-2_plusAHTc broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan growth condition Lysogeny Broth (LB) with anhydrotetracycline isolate not applicable organism part whole organism phenotype SPI-1 inactivation; Ptet activation sample name E-MTAB-11419:MA14358-2_plusAHTc strain MA14358 serovar Typhimurium sub_species enterica ERS10393953 SAMEA12788604 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788604 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA14302-2_plusARA broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry hilA::gfpSF ∆K28-kan growth condition Lysogeny Broth (LB) with arabinose isolate not applicable organism part whole organism phenotype NusG depletion sample name E-MTAB-11419:MA14302-2_plusARA strain MA14302 serovar Typhimurium sub_species enterica ERS10393976 SAMEA12788627 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788627 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA14358-4a_plusARA broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan growth condition Lysogeny Broth (LB) with arabinose isolate not applicable organism part whole organism phenotype SPI-1 inactivation; NusG depletion sample name E-MTAB-11419:MA14358-4a_plusARA strain MA14358 serovar Typhimurium sub_species enterica ERS10393980 SAMEA12788631 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788631 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA14358-4b_plusARA broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan growth condition Lysogeny Broth (LB) with arabinose isolate not applicable organism part whole organism phenotype SPI-1 inactivation; NusG depletion sample name E-MTAB-11419:MA14358-4b_plusARA strain MA14358 serovar Typhimurium sub_species enterica ERS10393964 SAMEA12788615 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). phenotype SPI-1 inactivation; NusG depletion strain MA14358 isolate not applicable ENA-FIRST-PUBLIC 2022-07-05T12:07:22Z organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ENA-LAST-UPDATE 2022-07-05T12:07:22Z growth condition Lysogeny Broth (LB) with arabinose scientific_name Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism part whole organism genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 ERS10393952 SAMEA12788603 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788603 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA14302-1_untreated broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry hilA::gfpSF ∆K28-kan growth condition Lysogeny Broth (LB) isolate not applicable organism part whole organism phenotype wild type sample name E-MTAB-11419:MA14302-1_untreated strain MA14302 serovar Typhimurium sub_species enterica ERS10393966 SAMEA12788617 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). phenotype SPI-1 inactivation strain MA14358 isolate not applicable ENA-FIRST-PUBLIC 2022-07-05T12:07:22Z organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ENA-LAST-UPDATE 2022-07-05T12:07:22Z growth condition Lysogeny Broth (LB) scientific_name Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism part whole organism genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 ERS10393950 SAMEA12788601 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). phenotype wild type strain MA12996 isolate not applicable ENA-FIRST-PUBLIC 2022-07-05T12:07:22Z organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ENA-LAST-UPDATE 2022-07-05T12:07:22Z growth condition Lysogeny Broth (LB) scientific_name Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 organism part whole organism genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 ERS10393960 SAMEA12788611 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788611 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA14358-1b_plusARA broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan growth condition Lysogeny Broth (LB) with arabinose isolate not applicable organism part whole organism phenotype SPI-1 inactivation; NusG depletion sample name E-MTAB-11419:MA14358-1b_plusARA strain MA14358 serovar Typhimurium sub_species enterica ERS10393951 SAMEA12788602 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction). ENA-FIRST-PUBLIC 2022-07-05 ENA-LAST-UPDATE 2022-07-05 External Id SAMEA12788602 INSDC center alias Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC center name Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University INSDC first public 2022-07-05T12:07:22Z INSDC last update 2022-07-05T12:07:22Z INSDC status public Submitter Id E-MTAB-11419:MA14302-1_plusARA broker name ArrayExpress genotype ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry hilA::gfpSF ∆K28-kan growth condition Lysogeny Broth (LB) with arabinose isolate not applicable organism part whole organism phenotype NusG depletion sample name E-MTAB-11419:MA14302-1_plusARA strain MA14302 serovar Typhimurium sub_species enterica