ERS2429795 SAMEA4609100 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C for 6 h. RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). Total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA larger than 17 nt was concentrated by Zymo RNA Clean & Concentrator 5. RNA was ligated to a 3' adenylated adapter using RNA ligase 2 and then to a 5' adapter using RNA ligase. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:47Z External Id SAMEA4609100 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:47Z INSDC status public Submitter Id E-MTAB-6704:5P-short-st-rnc-1 broker name ArrayExpress genotype drnc14::Tn10 growth condition stationary phase culture sample name E-MTAB-6704:5P-short-st-rnc-1 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429796 SAMEA4609101 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C for 6 h. RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). Total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA larger than 17 nt was concentrated by Zymo RNA Clean & Concentrator 5. RNA was ligated to a 3' adenylated adapter using RNA ligase 2 and then to a 5' adapter using RNA ligase. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609101 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-short-st-rnc-2 broker name ArrayExpress genotype drnc14::Tn10 growth condition stationary phase culture sample name E-MTAB-6704:5P-short-st-rnc-2 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429797 SAMEA4609102 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C for 6 h. RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). Total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA larger than 17 nt was concentrated by Zymo RNA Clean & Concentrator 5. RNA was ligated to a 3' adenylated adapter using RNA ligase 2 and then to a 5' adapter using RNA ligase. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609102 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-short-st-rnc-3 broker name ArrayExpress genotype drnc14::Tn10 growth condition stationary phase culture sample name E-MTAB-6704:5P-short-st-rnc-3 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429798 SAMEA4609103 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C for 6 h. RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). Total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA larger than 17 nt was concentrated by Zymo RNA Clean & Concentrator 5. RNA was ligated to a 3' adenylated adapter using RNA ligase 2 and then to a 5' adapter using RNA ligase. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609103 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-short-st-wt-1 broker name ArrayExpress genotype wild type genotype growth condition stationary phase culture sample name E-MTAB-6704:5P-short-st-wt-1 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429799 SAMEA4609104 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C for 6 h. RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). Total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA larger than 17 nt was concentrated by Zymo RNA Clean & Concentrator 5. RNA was ligated to a 3' adenylated adapter using RNA ligase 2 and then to a 5' adapter using RNA ligase. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609104 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-short-st-wt-2 broker name ArrayExpress genotype wild type genotype growth condition stationary phase culture sample name E-MTAB-6704:5P-short-st-wt-2 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429800 SAMEA4609105 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C for 6 h. RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). Total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA larger than 17 nt was concentrated by Zymo RNA Clean & Concentrator 5. RNA was ligated to a 3' adenylated adapter using RNA ligase 2 and then to a 5' adapter using RNA ligase. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609105 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-short-st-wt-3 broker name ArrayExpress genotype wild type genotype growth condition stationary phase culture sample name E-MTAB-6704:5P-short-st-wt-3 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429801 SAMEA4609106 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C to log phase (OD600 = 0.3) RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA was concentrated by Ampure XP beads. 3' end of the RNA was blocked by annealing of a 5' adenylated adapter using RNA ligase 2 truncated K227Q (New England Biolabs). 3' blocked RNA was ligated to a 5' adapter using RNA ligase 1 (New England Biolabs). The RNA was randomly trimmed using S1 nuclease (Thermo Scientific) at 22 °C. Trimming was stopped after 8 min by the addition of EDTA to a final concentration of 30 mM. RNA was then ligated to a 3' RNA adapter using RNA ligase 1. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609106 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-log-rnc-1 broker name ArrayExpress genotype drnc14::Tn10 growth condition logarithmic phase culture sample name E-MTAB-6704:5P-log-rnc-1 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429802 SAMEA4609107 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C to log phase (OD600 = 0.3) RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA was concentrated by Ampure XP beads. 3' end of the RNA was blocked by annealing of a 5' adenylated adapter using RNA ligase 2 truncated K227Q (New England Biolabs). 3' blocked RNA was ligated to a 5' adapter using RNA ligase 1 (New England Biolabs). The RNA was randomly trimmed using S1 nuclease (Thermo Scientific) at 22 °C. Trimming was stopped after 8 min by the addition of EDTA to a final concentration of 30 mM. RNA was then ligated to a 3' RNA adapter using RNA ligase 1. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609107 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-log-rnc-2 broker name ArrayExpress genotype drnc14::Tn10 growth condition logarithmic phase culture sample name E-MTAB-6704:5P-log-rnc-2 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429803 SAMEA4609108 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C to log phase (OD600 = 0.3) RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA was concentrated by Ampure XP beads. 3' end of the RNA was blocked by annealing of a 5' adenylated adapter using RNA ligase 2 truncated K227Q (New England Biolabs). 3' blocked RNA was ligated to a 5' adapter using RNA ligase 1 (New England Biolabs). The RNA was randomly trimmed using S1 nuclease (Thermo Scientific) at 22 °C. Trimming was stopped after 8 min by the addition of EDTA to a final concentration of 30 mM. RNA was then ligated to a 3' RNA adapter using RNA ligase 1. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609108 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-log-rnc-3 broker name ArrayExpress genotype drnc14::Tn10 growth condition logarithmic phase culture sample name E-MTAB-6704:5P-log-rnc-3 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429804 SAMEA4609109 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C to log phase (OD600 = 0.3) RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA was concentrated by Ampure XP beads. 3' end of the RNA was blocked by annealing of a 5' adenylated adapter using RNA ligase 2 truncated K227Q (New England Biolabs). 3' blocked RNA was ligated to a 5' adapter using RNA ligase 1 (New England Biolabs). The RNA was randomly trimmed using S1 nuclease (Thermo Scientific) at 22 °C. Trimming was stopped after 8 min by the addition of EDTA to a final concentration of 30 mM. RNA was then ligated to a 3' RNA adapter using RNA ligase 1. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609109 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-log-rnc-4 broker name ArrayExpress genotype drnc14::Tn10 growth condition logarithmic phase culture sample name E-MTAB-6704:5P-log-rnc-4 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429805 SAMEA4609110 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C for 6 h. RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA was concentrated by Ampure XP beads. 3' end of the RNA was blocked by annealing of a 5' adenylated adapter using RNA ligase 2 truncated K227Q (New England Biolabs). 3' blocked RNA was ligated to a 5' adapter using RNA ligase 1 (New England Biolabs). The RNA was randomly trimmed using S1 nuclease (Thermo Scientific) at 22 °C. Trimming was stopped after 8 min by the addition of EDTA to a final concentration of 30 mM. RNA was then ligated to a 3' RNA adapter using RNA ligase 1. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609110 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-st-rnc-1 broker name ArrayExpress genotype drnc14::Tn10 growth condition stationary phase culture sample name E-MTAB-6704:5P-st-rnc-1 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429806 SAMEA4609111 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C for 6 h. RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA was concentrated by Ampure XP beads. 3' end of the RNA was blocked by annealing of a 5' adenylated adapter using RNA ligase 2 truncated K227Q (New England Biolabs). 3' blocked RNA was ligated to a 5' adapter using RNA ligase 1 (New England Biolabs). The RNA was randomly trimmed using S1 nuclease (Thermo Scientific) at 22 °C. Trimming was stopped after 8 min by the addition of EDTA to a final concentration of 30 mM. RNA was then ligated to a 3' RNA adapter using RNA ligase 1. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609111 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-st-rnc-2 broker name ArrayExpress genotype drnc14::Tn10 growth condition stationary phase culture sample name E-MTAB-6704:5P-st-rnc-2 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429807 SAMEA4609112 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C for 6 h. RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA was concentrated by Ampure XP beads. 3' end of the RNA was blocked by annealing of a 5' adenylated adapter using RNA ligase 2 truncated K227Q (New England Biolabs). 3' blocked RNA was ligated to a 5' adapter using RNA ligase 1 (New England Biolabs). The RNA was randomly trimmed using S1 nuclease (Thermo Scientific) at 22 °C. Trimming was stopped after 8 min by the addition of EDTA to a final concentration of 30 mM. RNA was then ligated to a 3' RNA adapter using RNA ligase 1. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609112 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-st-rnc-3 broker name ArrayExpress genotype drnc14::Tn10 growth condition stationary phase culture sample name E-MTAB-6704:5P-st-rnc-3 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429808 SAMEA4609113 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C to log phase (OD600 = 0.3) RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA was concentrated by Ampure XP beads. 3' end of the RNA was blocked by annealing of a 5' adenylated adapter using RNA ligase 2 truncated K227Q (New England Biolabs). 3' blocked RNA was ligated to a 5' adapter using RNA ligase 1 (New England Biolabs). The RNA was randomly trimmed using S1 nuclease (Thermo Scientific) at 22 °C. Trimming was stopped after 8 min by the addition of EDTA to a final concentration of 30 mM. RNA was then ligated to a 3' RNA adapter using RNA ligase 1. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609113 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-log-wt-1 broker name ArrayExpress genotype wild type genotype growth condition logarithmic phase culture sample name E-MTAB-6704:5P-log-wt-1 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429809 SAMEA4609114 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C to log phase (OD600 = 0.3) RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA was concentrated by Ampure XP beads. 3' end of the RNA was blocked by annealing of a 5' adenylated adapter using RNA ligase 2 truncated K227Q (New England Biolabs). 3' blocked RNA was ligated to a 5' adapter using RNA ligase 1 (New England Biolabs). The RNA was randomly trimmed using S1 nuclease (Thermo Scientific) at 22 °C. Trimming was stopped after 8 min by the addition of EDTA to a final concentration of 30 mM. RNA was then ligated to a 3' RNA adapter using RNA ligase 1. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609114 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-log-wt-2 broker name ArrayExpress genotype wild type genotype growth condition logarithmic phase culture sample name E-MTAB-6704:5P-log-wt-2 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429810 SAMEA4609115 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C to log phase (OD600 = 0.3) RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA was concentrated by Ampure XP beads. 3' end of the RNA was blocked by annealing of a 5' adenylated adapter using RNA ligase 2 truncated K227Q (New England Biolabs). 3' blocked RNA was ligated to a 5' adapter using RNA ligase 1 (New England Biolabs). The RNA was randomly trimmed using S1 nuclease (Thermo Scientific) at 22 °C. Trimming was stopped after 8 min by the addition of EDTA to a final concentration of 30 mM. RNA was then ligated to a 3' RNA adapter using RNA ligase 1. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609115 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-log-wt-3 broker name ArrayExpress genotype wild type genotype growth condition logarithmic phase culture sample name E-MTAB-6704:5P-log-wt-3 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429811 SAMEA4609116 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C for 6 h. RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA was concentrated by Ampure XP beads. 3' end of the RNA was blocked by annealing of a 5' adenylated adapter using RNA ligase 2 truncated K227Q (New England Biolabs). 3' blocked RNA was ligated to a 5' adapter using RNA ligase 1 (New England Biolabs). The RNA was randomly trimmed using S1 nuclease (Thermo Scientific) at 22 °C. Trimming was stopped after 8 min by the addition of EDTA to a final concentration of 30 mM. RNA was then ligated to a 3' RNA adapter using RNA ligase 1. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609116 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-st-wt-1 broker name ArrayExpress genotype wild type genotype growth condition stationary phase culture sample name E-MTAB-6704:5P-st-wt-1 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429812 SAMEA4609117 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C for 6 h. RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA was concentrated by Ampure XP beads. 3' end of the RNA was blocked by annealing of a 5' adenylated adapter using RNA ligase 2 truncated K227Q (New England Biolabs). 3' blocked RNA was ligated to a 5' adapter using RNA ligase 1 (New England Biolabs). The RNA was randomly trimmed using S1 nuclease (Thermo Scientific) at 22 °C. Trimming was stopped after 8 min by the addition of EDTA to a final concentration of 30 mM. RNA was then ligated to a 3' RNA adapter using RNA ligase 1. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609117 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-st-wt-2 broker name ArrayExpress genotype wild type genotype growth condition stationary phase culture sample name E-MTAB-6704:5P-st-wt-2 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429813 SAMEA4609118 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C for 6 h. RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA was concentrated by Ampure XP beads. 3' end of the RNA was blocked by annealing of a 5' adenylated adapter using RNA ligase 2 truncated K227Q (New England Biolabs). 3' blocked RNA was ligated to a 5' adapter using RNA ligase 1 (New England Biolabs). The RNA was randomly trimmed using S1 nuclease (Thermo Scientific) at 22 °C. Trimming was stopped after 8 min by the addition of EDTA to a final concentration of 30 mM. RNA was then ligated to a 3' RNA adapter using RNA ligase 1. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609118 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-st-wt-3 broker name ArrayExpress genotype wild type genotype growth condition stationary phase culture sample name E-MTAB-6704:5P-st-wt-3 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429814 SAMEA4609119 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C to log phase (OD600 = 0.3) RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). Total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA larger than 17 nt was concentrated by Zymo RNA Clean & Concentrator 5. RNA was ligated to a 3' adenylated adapter using RNA ligase 2 and then to a 5' adapter using RNA ligase. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609119 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-short-log-rnc-1 broker name ArrayExpress genotype drnc14::Tn10 growth condition logarithmic phase culture sample name E-MTAB-6704:5P-short-log-rnc-1 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429815 SAMEA4609120 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C to log phase (OD600 = 0.3) RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). Total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA larger than 17 nt was concentrated by Zymo RNA Clean & Concentrator 5. RNA was ligated to a 3' adenylated adapter using RNA ligase 2 and then to a 5' adapter using RNA ligase. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609120 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-short-log-rnc-2 broker name ArrayExpress genotype drnc14::Tn10 growth condition logarithmic phase culture sample name E-MTAB-6704:5P-short-log-rnc-2 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429816 SAMEA4609121 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C to log phase (OD600 = 0.3) RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). Total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA larger than 17 nt was concentrated by Zymo RNA Clean & Concentrator 5. RNA was ligated to a 3' adenylated adapter using RNA ligase 2 and then to a 5' adapter using RNA ligase. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609121 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-short-log-rnc-3 broker name ArrayExpress genotype drnc14::Tn10 growth condition logarithmic phase culture sample name E-MTAB-6704:5P-short-log-rnc-3 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429817 SAMEA4609122 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C to log phase (OD600 = 0.3) RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). Total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA larger than 17 nt was concentrated by Zymo RNA Clean & Concentrator 5. RNA was ligated to a 3' adenylated adapter using RNA ligase 2 and then to a 5' adapter using RNA ligase. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609122 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-short-log-wt-1 broker name ArrayExpress genotype wild type genotype growth condition logarithmic phase culture sample name E-MTAB-6704:5P-short-log-wt-1 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429818 SAMEA4609123 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C to log phase (OD600 = 0.3) RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). Total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA larger than 17 nt was concentrated by Zymo RNA Clean & Concentrator 5. RNA was ligated to a 3' adenylated adapter using RNA ligase 2 and then to a 5' adapter using RNA ligase. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609123 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-short-log-wt-2 broker name ArrayExpress genotype wild type genotype growth condition logarithmic phase culture sample name E-MTAB-6704:5P-short-log-wt-2 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429819 SAMEA4609124 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C to log phase (OD600 = 0.3) RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). Total RNA was treated with TURBO DNase (Invitrogen) according to manufacturer instructions. DNase treated RNA was subjected to ribosomal RNA depletion using Ribo-Zero magnetic kit (Illumina). rRNA depleted RNA larger than 17 nt was concentrated by Zymo RNA Clean & Concentrator 5. RNA was ligated to a 3' adenylated adapter using RNA ligase 2 and then to a 5' adapter using RNA ligase. cDNA was amplified using Illumina compatible indexed primers and cleaned-up with 1X Ampure XP beads. ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609124 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:5P-short-log-wt-3 broker name ArrayExpress genotype wild type genotype growth condition logarithmic phase culture sample name E-MTAB-6704:5P-short-log-wt-3 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429820 SAMEA4609125 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C to log phase (OD600 = 0.3) RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). RNAtag-Seq protocol (Shishkin et al., 2015) ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609125 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:Total-log-rnc-1 broker name ArrayExpress genotype drnc14::Tn10 growth condition logarithmic phase culture sample name E-MTAB-6704:Total-log-rnc-1 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429821 SAMEA4609126 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C to log phase (OD600 = 0.3) RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). RNAtag-Seq protocol (Shishkin et al., 2015) ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609126 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:Total-log-rnc-2 broker name ArrayExpress genotype drnc14::Tn10 growth condition logarithmic phase culture sample name E-MTAB-6704:Total-log-rnc-2 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429822 SAMEA4609127 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C to log phase (OD600 = 0.3) RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). RNAtag-Seq protocol (Shishkin et al., 2015) ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609127 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:Total-log-rnc-3 broker name ArrayExpress genotype drnc14::Tn10 growth condition logarithmic phase culture sample name E-MTAB-6704:Total-log-rnc-3 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429823 SAMEA4609128 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C for 6 h. RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). RNAtag-Seq protocol (Shishkin et al., 2015) ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609128 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:Total-st-rnc-1 broker name ArrayExpress genotype drnc14::Tn10 growth condition stationary phase culture sample name E-MTAB-6704:Total-st-rnc-1 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429824 SAMEA4609129 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C for 6 h. RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). RNAtag-Seq protocol (Shishkin et al., 2015) ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609129 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:Total-st-rnc-2 broker name ArrayExpress genotype drnc14::Tn10 growth condition stationary phase culture sample name E-MTAB-6704:Total-st-rnc-2 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429825 SAMEA4609130 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C for 6 h. RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). RNAtag-Seq protocol (Shishkin et al., 2015) ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609130 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:Total-st-rnc-3 broker name ArrayExpress genotype drnc14::Tn10 growth condition stationary phase culture sample name E-MTAB-6704:Total-st-rnc-3 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429826 SAMEA4609131 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C to log phase (OD600 = 0.3) RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). RNAtag-Seq protocol (Shishkin et al., 2015) ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609131 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:Total-log-wt-1 broker name ArrayExpress genotype wild type genotype growth condition logarithmic phase culture sample name E-MTAB-6704:Total-log-wt-1 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429827 SAMEA4609132 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C to log phase (OD600 = 0.3) RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). RNAtag-Seq protocol (Shishkin et al., 2015) ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609132 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:Total-log-wt-2 broker name ArrayExpress genotype wild type genotype growth condition logarithmic phase culture sample name E-MTAB-6704:Total-log-wt-2 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429828 SAMEA4609133 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C to log phase (OD600 = 0.3) RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). RNAtag-Seq protocol (Shishkin et al., 2015) ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609133 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:Total-log-wt-3 broker name ArrayExpress genotype wild type genotype growth condition logarithmic phase culture sample name E-MTAB-6704:Total-log-wt-3 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429829 SAMEA4609134 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C for 6 h. RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). RNAtag-Seq protocol (Shishkin et al., 2015) ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609134 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:Total-st-wt-1 broker name ArrayExpress genotype wild type genotype growth condition stationary phase culture sample name E-MTAB-6704:Total-st-wt-1 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429830 SAMEA4609135 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C for 6 h. RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). RNAtag-Seq protocol (Shishkin et al., 2015) ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609135 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:Total-st-wt-2 broker name ArrayExpress genotype wild type genotype growth condition stationary phase culture sample name E-MTAB-6704:Total-st-wt-2 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655 ERS2429831 SAMEA4609136 511145 Escherichia coli str. K-12 substr. MG1655 Protocols: Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (Sigma Aldrich) in a final concentration of 0.9 mg/ml and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze in 37 °C and in liquid nitrogen, respectively. E .coli Strains MG1655 and MG1655 Δrnc14::Tn10 were grown overnight in LB at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB, and re-grown with shaking at 37 °C for 6 h. RNA was extracted according to the standard Tri-Reagent protocol (Sigma Aldrich). RNAtag-Seq protocol (Shishkin et al., 2015) ENA-FIRST-PUBLIC 2018-09-30T17:01:59Z ENA-LAST-UPDATE 2018-04-24T16:45:48Z External Id SAMEA4609136 INSDC center name Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem. INSDC first public 2018-09-30T17:01:59Z INSDC last update 2018-04-24T16:45:48Z INSDC status public Submitter Id E-MTAB-6704:Total-st-wt-3 broker name ArrayExpress genotype wild type genotype growth condition stationary phase culture sample name E-MTAB-6704:Total-st-wt-3 scientific_name Escherichia coli str. K-12 substr. MG1655 strain K-12 substrain MG1655