ERX7846470 E-MTAB-11419:MA14358-3a_plusARA_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393968 SAMEA12788619 MA14358-3a_plusARA_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation; NusG depletion ERX7846450 E-MTAB-11419:MA12996-2a_untreated_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393948 SAMEA12788599 MA12996-2a_untreated_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA12996 Experimental Factor: phenotype wild type ERX7846467 E-MTAB-11419:MA14358-2_plusARA_plusAHTc_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393965 SAMEA12788616 MA14358-2_plusARA_plusAHTc_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation; NusG depletion; Ptet activation ERX7846473 E-MTAB-11419:MA14358-3b_plusAHTc_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393971 SAMEA12788622 MA14358-3b_plusAHTc_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation; Ptet activation ERX7846445 E-MTAB-11419:MA12996-1a_plusARA_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393943 SAMEA12788594 MA12996-1a_plusARA_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA12996 Experimental Factor: phenotype NusG depletion ERX7846484 E-MTAB-11419:MA14358-4b_untreated_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393982 SAMEA12788633 MA14358-4b_untreated_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation ERX7846474 E-MTAB-11419:MA14358-3b_plusARA_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393972 SAMEA12788623 MA14358-3b_plusARA_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation; NusG depletion ERX7846456 E-MTAB-11419:MA14302-2_untreated_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393954 SAMEA12788605 MA14302-2_untreated_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14302 Experimental Factor: phenotype wild type ERX7846457 E-MTAB-11419:MA14358-1a_plusAHTc_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393955 SAMEA12788606 MA14358-1a_plusAHTc_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation; Ptet activation ERX7846449 E-MTAB-11419:MA12996-2a_plusARA_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393947 SAMEA12788598 MA12996-2a_plusARA_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA12996 Experimental Factor: phenotype NusG depletion ERX7846469 E-MTAB-11419:MA14358-3a_plusAHTc_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393967 SAMEA12788618 MA14358-3a_plusAHTc_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation; Ptet activation ERX7846458 E-MTAB-11419:MA14358-1a_plusARA_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393956 SAMEA12788607 MA14358-1a_plusARA_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation; NusG depletion ERX7846471 E-MTAB-11419:MA14358-3a_plusARA_plusAHTc_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393969 SAMEA12788620 MA14358-3a_plusARA_plusAHTc_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation; NusG depletion; Ptet activation ERX7846483 E-MTAB-11419:MA14358-4b_plusARA_plusAHTc_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393981 SAMEA12788632 MA14358-4b_plusARA_plusAHTc_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation; NusG depletion; Ptet activation ERX7846461 E-MTAB-11419:MA14358-1b_plusAHTc_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393959 SAMEA12788610 MA14358-1b_plusAHTc_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation; Ptet activation ERX7846466 E-MTAB-11419:MA14358-2_plusARA_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393964 SAMEA12788615 MA14358-2_plusARA_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation; NusG depletion ERX7846463 E-MTAB-11419:MA14358-1b_plusARA_plusAHTc_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393961 SAMEA12788612 MA14358-1b_plusARA_plusAHTc_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation; NusG depletion; Ptet activation ERX7846479 E-MTAB-11419:MA14358-4a_plusARA_plusAHTc_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393977 SAMEA12788628 MA14358-4a_plusARA_plusAHTc_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation; NusG depletion; Ptet activation ERX7846446 E-MTAB-11419:MA12996-1a_untreated_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393944 SAMEA12788595 MA12996-1a_untreated_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA12996 Experimental Factor: phenotype wild type ERX7846475 E-MTAB-11419:MA14358-3b_plusARA_plusAHTc_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393973 SAMEA12788624 MA14358-3b_plusARA_plusAHTc_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation; NusG depletion; Ptet activation ERX7846468 E-MTAB-11419:MA14358-2_untreated_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393966 SAMEA12788617 MA14358-2_untreated_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation ERX7846465 E-MTAB-11419:MA14358-2_plusAHTc_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393963 SAMEA12788614 MA14358-2_plusAHTc_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation; Ptet activation ERX7846460 E-MTAB-11419:MA14358-1a_untreated_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393958 SAMEA12788609 MA14358-1a_untreated_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation ERX7846454 E-MTAB-11419:MA14302-1_untreated_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393952 SAMEA12788603 MA14302-1_untreated_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14302 Experimental Factor: phenotype wild type ERX7846452 E-MTAB-11419:MA12996-2b_untreated_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393950 SAMEA12788601 MA12996-2b_untreated_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA12996 Experimental Factor: phenotype wild type ERX7846481 E-MTAB-11419:MA14358-4b_plusAHTc_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393979 SAMEA12788630 MA14358-4b_plusAHTc_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation; Ptet activation ERX7846478 E-MTAB-11419:MA14358-4a_plusARA_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393976 SAMEA12788627 MA14358-4a_plusARA_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation; NusG depletion ERX7846472 E-MTAB-11419:MA14358-3a_untreated_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393970 SAMEA12788621 MA14358-3a_untreated_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation ERX7846459 E-MTAB-11419:MA14358-1a_plusARA_plusAHTc_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393957 SAMEA12788608 MA14358-1a_plusARA_plusAHTc_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation; NusG depletion; Ptet activation ERX7846480 E-MTAB-11419:MA14358-4a_untreated_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393978 SAMEA12788629 MA14358-4a_untreated_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation ERX7846451 E-MTAB-11419:MA12996-2b_plusARA_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393949 SAMEA12788600 MA12996-2b_plusARA_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA12996 Experimental Factor: phenotype NusG depletion ERX7846464 E-MTAB-11419:MA14358-1b_untreated_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393962 SAMEA12788613 MA14358-1b_untreated_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation ERX7846476 E-MTAB-11419:MA14358-3b_untreated_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393974 SAMEA12788625 MA14358-3b_untreated_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation ERX7846462 E-MTAB-11419:MA14358-1b_plusARA_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393960 SAMEA12788611 MA14358-1b_plusARA_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation; NusG depletion ERX7846455 E-MTAB-11419:MA14302-2_plusARA_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393953 SAMEA12788604 MA14302-2_plusARA_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14302 Experimental Factor: phenotype NusG depletion ERX7846482 E-MTAB-11419:MA14358-4b_plusARA_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393980 SAMEA12788631 MA14358-4b_plusARA_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation; NusG depletion ERX7846447 E-MTAB-11419:MA12996-1b_plusARA_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393945 SAMEA12788596 MA12996-1b_plusARA_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA12996 Experimental Factor: phenotype NusG depletion ERX7846453 E-MTAB-11419:MA14302-1_plusARA_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393951 SAMEA12788602 MA14302-1_plusARA_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14302 Experimental Factor: phenotype NusG depletion ERX7846448 E-MTAB-11419:MA12996-1b_untreated_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393946 SAMEA12788597 MA12996-1b_untreated_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA12996 Experimental Factor: phenotype wild type ERX7846477 E-MTAB-11419:MA14358-4a_plusAHTc_p ERP135168 PRJEB50575 Measuring the effects of pervasive transcription on promoter activity in Salmonella Pathogenicity Island 1 by semiquantitative 5'RACE-Seq ERS10393975 SAMEA12788626 MA14358-4a_plusAHTc_p AMPLICON TRANSCRIPTOMIC RT-PCR 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). NextSeq 500 Experimental Factor: strain MA14358 Experimental Factor: phenotype SPI-1 inactivation; Ptet activation