All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: Ribosome protected mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
Ribosome profiling at 37°C in WT cells_1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 37°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: Ribosome protected mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
Ribosome profiling 10 min after shift to 10°C in WT cells_1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: Ribosome protected mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
Ribosome profiling 30 min after shift to 10°C in WT cells PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: Ribosome protected mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
Ribosome profiling 2 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: Ribosome protected mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
Ribosome profiling 3 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: Ribosome protected mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
Ribosome profiling 4 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: Ribosome protected mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
Ribosome profiling 6 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: Ribosome protected mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
Ribosome profiling 5 min after shift to 10°C in WT cells PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: Ribosome protected mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
Ribosome profiling 10 min after shift to 10°C in WT cells_2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: Ribosome protected mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
Ribosome profiling 15 min after shift to 10°C in WT cells PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: Ribosome protected mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
Ribosome profiling at 37°C in WT cells_2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 37°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: {delta}cspABCEG PGCGROWTHCONDITIONS
MG1655 ∆cspABCEG PGCGROWTHCONDITIONS
molecule subtype: Ribosome protected mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
Ribosome profiling at 37°C in ∆cspABCEG cells PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 37°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
mRNA-seq at 37°C in WT cells_1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 37°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
mRNA-seq 10 min after shift to 10°C in WT cells PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
mRNA-seq 30 min after shift to 10°C in WT cells PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
mRNA-seq 2 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
mRNA-seq 3 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
mRNA-seq 4 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
mRNA-seq 6 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
mRNA-seq 8 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: {delta}cspABEG PGCGROWTHCONDITIONS
MG1655 ∆cspABEG PGCGROWTHCONDITIONS
molecule subtype: mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
mRNA-seq 8 hr after shift to 10°C in ∆cspABEG cells PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
mRNA-seq at 37°C in WT cells_2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 37°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: {delta}cspABCEG PGCGROWTHCONDITIONS
MG1655 ∆cspABCEG PGCGROWTHCONDITIONS
molecule subtype: mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
mRNA-seq at 37°C in ∆cspABCEG cells PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 37°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
DMS-seq 30 min after shift to 10°C in WT cells PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: DMS-modified mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
DMS-seq 6 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: DMS-modified mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
DMS-seq 8 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: DMS-modified mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
DMS-seq 8 hr after shift to 10°C in ∆cspABEG cells PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: {delta}cspABEG PGCGROWTHCONDITIONS
MG1655 ∆cspABEG PGCGROWTHCONDITIONS
molecule subtype: DMS-modified mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
DMS-seq 8 hr after shift to 10°C in ∆cspBG cells PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: {delta}cspBG PGCGROWTHCONDITIONS
MG1655 ∆cspBG PGCGROWTHCONDITIONS
molecule subtype: DMS-modified mRNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: Total RNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Total RNA-seq 20 min after shift to 10°C in WT cells PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: Total RNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Total RNA-seq 4 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: Total RNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Total RNA-seq 8 hr after shift to 10°C in WT cells PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: {delta}rnr PGCGROWTHCONDITIONS
MG1655 ∆rnr PGCGROWTHCONDITIONS
molecule subtype: Total RNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Total RNA-seq 20 min after shift to 10°C in ∆rnr cells PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: {delta}rnr PGCGROWTHCONDITIONS
MG1655 ∆rnr PGCGROWTHCONDITIONS
molecule subtype: Total RNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Total RNA-seq 4 hr after shift to 10°C in ∆rnr cells PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
genotype/variation: {delta}rnr PGCGROWTHCONDITIONS
MG1655 ∆rnr PGCGROWTHCONDITIONS
molecule subtype: Total RNA PGCGROWTHCONDITIONS
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
temperature: 10°C PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Total RNA-seq 8 hr after shift to 10°C in ∆rnr cells PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
Aligned reads were designated to top and bottom strands using Samtools PGCGROWTHCONDITIONS
At the appropriate optical density, culture growth was instantaneously arrested by addition of an equal volume of chilled 100% ethanol, and the cells were stored at –80°C until they were processed for RNA extraction. The cells were lysed and total RNA was prepared by the hot phenol method essentially as described, after chromosomal DNA has been digested with RNase-free DNase. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
bcl2fastq2 v2.15.0 (Demultiplexing), Fastqc 0.11.5 (read quality), Cutadapt-1.9.1 (adaptor trimming) PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genome_build: NC000913.2 MG1655 PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
Reads were aligned using MG15655 as reference genome (NC000913.2) using Bowtie2 tool. PGCGROWTHCONDITIONS
ssRNA-seq PGCGROWTHCONDITIONS
Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS
Strand specific base read counts were determined for each of 4091 ORFs for the 15 samples PGCGROWTHCONDITIONS
Strand-specific RNA-Seq data were generated, following rRNA depletion with a Ribo-Zero kit, with the aid of the di-tagged cDNA strategy (ScriptSeq) on an Illumina NextSeq platform PGCGROWTHCONDITIONS
substrain: GJ13519 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The text file contains sense and antisense raw base read counts for each of the 4091 ORFs for all the 15 samples, and the explanation key is included in the file. PGCGROWTHCONDITIONS
Viable clones of the UvsW-expressing strains GJ13531 (Δrho) and GJ13507 (ΔnusG) were obtained as white colonies from their respective shelter plasmid-carrying derivatives GJ13531/pHYD2411 and GJ13507 /pHYD2412 on glucose-minimal A plates supplemented with Xgal and IPTG at 200 μM (for Δrho) or 3 μM (for ΔnusG), as previously described PGCGROWTHCONDITIONS
WT glucose_replicate1 PGCGROWTHCONDITIONS
Aligned reads were designated to top and bottom strands using Samtools PGCGROWTHCONDITIONS
At the appropriate optical density, culture growth was instantaneously arrested by addition of an equal volume of chilled 100% ethanol, and the cells were stored at –80°C until they were processed for RNA extraction. The cells were lysed and total RNA was prepared by the hot phenol method essentially as described, after chromosomal DNA has been digested with RNase-free DNase. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
bcl2fastq2 v2.15.0 (Demultiplexing), Fastqc 0.11.5 (read quality), Cutadapt-1.9.1 (adaptor trimming) PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genome_build: NC000913.2 MG1655 PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
Reads were aligned using MG15655 as reference genome (NC000913.2) using Bowtie2 tool. PGCGROWTHCONDITIONS
ssRNA-seq PGCGROWTHCONDITIONS
Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS
Strand specific base read counts were determined for each of 4091 ORFs for the 15 samples PGCGROWTHCONDITIONS
Strand-specific RNA-Seq data were generated, following rRNA depletion with a Ribo-Zero kit, with the aid of the di-tagged cDNA strategy (ScriptSeq) on an Illumina NextSeq platform PGCGROWTHCONDITIONS
substrain: GJ13519 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The text file contains sense and antisense raw base read counts for each of the 4091 ORFs for all the 15 samples, and the explanation key is included in the file. PGCGROWTHCONDITIONS
Viable clones of the UvsW-expressing strains GJ13531 (Δrho) and GJ13507 (ΔnusG) were obtained as white colonies from their respective shelter plasmid-carrying derivatives GJ13531/pHYD2411 and GJ13507 /pHYD2412 on glucose-minimal A plates supplemented with Xgal and IPTG at 200 μM (for Δrho) or 3 μM (for ΔnusG), as previously described PGCGROWTHCONDITIONS
WT glucose_replicate2 PGCGROWTHCONDITIONS
Aligned reads were designated to top and bottom strands using Samtools PGCGROWTHCONDITIONS
At the appropriate optical density, culture growth was instantaneously arrested by addition of an equal volume of chilled 100% ethanol, and the cells were stored at –80°C until they were processed for RNA extraction. The cells were lysed and total RNA was prepared by the hot phenol method essentially as described, after chromosomal DNA has been digested with RNase-free DNase. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
bcl2fastq2 v2.15.0 (Demultiplexing), Fastqc 0.11.5 (read quality), Cutadapt-1.9.1 (adaptor trimming) PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genome_build: NC000913.2 MG1655 PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
Reads were aligned using MG15655 as reference genome (NC000913.2) using Bowtie2 tool. PGCGROWTHCONDITIONS
ssRNA-seq PGCGROWTHCONDITIONS
Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS
Strand specific base read counts were determined for each of 4091 ORFs for the 15 samples PGCGROWTHCONDITIONS
Strand-specific RNA-Seq data were generated, following rRNA depletion with a Ribo-Zero kit, with the aid of the di-tagged cDNA strategy (ScriptSeq) on an Illumina NextSeq platform PGCGROWTHCONDITIONS
substrain: GJ13519 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The text file contains sense and antisense raw base read counts for each of the 4091 ORFs for all the 15 samples, and the explanation key is included in the file. PGCGROWTHCONDITIONS
Viable clones of the UvsW-expressing strains GJ13531 (Δrho) and GJ13507 (ΔnusG) were obtained as white colonies from their respective shelter plasmid-carrying derivatives GJ13531/pHYD2411 and GJ13507 /pHYD2412 on glucose-minimal A plates supplemented with Xgal and IPTG at 200 μM (for Δrho) or 3 μM (for ΔnusG), as previously described PGCGROWTHCONDITIONS
WT glucose_replicate3 PGCGROWTHCONDITIONS
Aligned reads were designated to top and bottom strands using Samtools PGCGROWTHCONDITIONS
At the appropriate optical density, culture growth was instantaneously arrested by addition of an equal volume of chilled 100% ethanol, and the cells were stored at –80°C until they were processed for RNA extraction. The cells were lysed and total RNA was prepared by the hot phenol method essentially as described, after chromosomal DNA has been digested with RNase-free DNase. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
bcl2fastq2 v2.15.0 (Demultiplexing), Fastqc 0.11.5 (read quality), Cutadapt-1.9.1 (adaptor trimming) PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genome_build: NC000913.2 MG1655 PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
Reads were aligned using MG15655 as reference genome (NC000913.2) using Bowtie2 tool. PGCGROWTHCONDITIONS
ssRNA-seq PGCGROWTHCONDITIONS
Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS
Strand specific base read counts were determined for each of 4091 ORFs for the 15 samples PGCGROWTHCONDITIONS
Strand-specific RNA-Seq data were generated, following rRNA depletion with a Ribo-Zero kit, with the aid of the di-tagged cDNA strategy (ScriptSeq) on an Illumina NextSeq platform PGCGROWTHCONDITIONS
substrain: GJ13519 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The text file contains sense and antisense raw base read counts for each of the 4091 ORFs for all the 15 samples, and the explanation key is included in the file. PGCGROWTHCONDITIONS
Viable clones of the UvsW-expressing strains GJ13531 (Δrho) and GJ13507 (ΔnusG) were obtained as white colonies from their respective shelter plasmid-carrying derivatives GJ13531/pHYD2411 and GJ13507 /pHYD2412 on glucose-minimal A plates supplemented with Xgal and IPTG at 200 μM (for Δrho) or 3 μM (for ΔnusG), as previously described PGCGROWTHCONDITIONS
WT_glycerol_replicate1 PGCGROWTHCONDITIONS
Aligned reads were designated to top and bottom strands using Samtools PGCGROWTHCONDITIONS
At the appropriate optical density, culture growth was instantaneously arrested by addition of an equal volume of chilled 100% ethanol, and the cells were stored at –80°C until they were processed for RNA extraction. The cells were lysed and total RNA was prepared by the hot phenol method essentially as described, after chromosomal DNA has been digested with RNase-free DNase. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
bcl2fastq2 v2.15.0 (Demultiplexing), Fastqc 0.11.5 (read quality), Cutadapt-1.9.1 (adaptor trimming) PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genome_build: NC000913.2 MG1655 PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
Reads were aligned using MG15655 as reference genome (NC000913.2) using Bowtie2 tool. PGCGROWTHCONDITIONS
ssRNA-seq PGCGROWTHCONDITIONS
Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS
Strand specific base read counts were determined for each of 4091 ORFs for the 15 samples PGCGROWTHCONDITIONS
Strand-specific RNA-Seq data were generated, following rRNA depletion with a Ribo-Zero kit, with the aid of the di-tagged cDNA strategy (ScriptSeq) on an Illumina NextSeq platform PGCGROWTHCONDITIONS
substrain: GJ13519 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The text file contains sense and antisense raw base read counts for each of the 4091 ORFs for all the 15 samples, and the explanation key is included in the file. PGCGROWTHCONDITIONS
Viable clones of the UvsW-expressing strains GJ13531 (Δrho) and GJ13507 (ΔnusG) were obtained as white colonies from their respective shelter plasmid-carrying derivatives GJ13531/pHYD2411 and GJ13507 /pHYD2412 on glucose-minimal A plates supplemented with Xgal and IPTG at 200 μM (for Δrho) or 3 μM (for ΔnusG), as previously described PGCGROWTHCONDITIONS
WT_glycerol_replicate2 PGCGROWTHCONDITIONS
Aligned reads were designated to top and bottom strands using Samtools PGCGROWTHCONDITIONS
At the appropriate optical density, culture growth was instantaneously arrested by addition of an equal volume of chilled 100% ethanol, and the cells were stored at –80°C until they were processed for RNA extraction. The cells were lysed and total RNA was prepared by the hot phenol method essentially as described, after chromosomal DNA has been digested with RNase-free DNase. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
bcl2fastq2 v2.15.0 (Demultiplexing), Fastqc 0.11.5 (read quality), Cutadapt-1.9.1 (adaptor trimming) PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genome_build: NC000913.2 MG1655 PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
Reads were aligned using MG15655 as reference genome (NC000913.2) using Bowtie2 tool. PGCGROWTHCONDITIONS
ssRNA-seq PGCGROWTHCONDITIONS
Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS
Strand specific base read counts were determined for each of 4091 ORFs for the 15 samples PGCGROWTHCONDITIONS
Strand-specific RNA-Seq data were generated, following rRNA depletion with a Ribo-Zero kit, with the aid of the di-tagged cDNA strategy (ScriptSeq) on an Illumina NextSeq platform PGCGROWTHCONDITIONS
substrain: GJ13519 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The text file contains sense and antisense raw base read counts for each of the 4091 ORFs for all the 15 samples, and the explanation key is included in the file. PGCGROWTHCONDITIONS
Viable clones of the UvsW-expressing strains GJ13531 (Δrho) and GJ13507 (ΔnusG) were obtained as white colonies from their respective shelter plasmid-carrying derivatives GJ13531/pHYD2411 and GJ13507 /pHYD2412 on glucose-minimal A plates supplemented with Xgal and IPTG at 200 μM (for Δrho) or 3 μM (for ΔnusG), as previously described PGCGROWTHCONDITIONS
WT_glycerol_replicate3 PGCGROWTHCONDITIONS
Aligned reads were designated to top and bottom strands using Samtools PGCGROWTHCONDITIONS
At the appropriate optical density, culture growth was instantaneously arrested by addition of an equal volume of chilled 100% ethanol, and the cells were stored at –80°C until they were processed for RNA extraction. The cells were lysed and total RNA was prepared by the hot phenol method essentially as described, after chromosomal DNA has been digested with RNase-free DNase. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
bcl2fastq2 v2.15.0 (Demultiplexing), Fastqc 0.11.5 (read quality), Cutadapt-1.9.1 (adaptor trimming) PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genome_build: NC000913.2 MG1655 PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
Reads were aligned using MG15655 as reference genome (NC000913.2) using Bowtie2 tool. PGCGROWTHCONDITIONS
ssRNA-seq PGCGROWTHCONDITIONS
Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS
Strand specific base read counts were determined for each of 4091 ORFs for the 15 samples PGCGROWTHCONDITIONS
Strand-specific RNA-Seq data were generated, following rRNA depletion with a Ribo-Zero kit, with the aid of the di-tagged cDNA strategy (ScriptSeq) on an Illumina NextSeq platform PGCGROWTHCONDITIONS
substrain: GJ13533 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The text file contains sense and antisense raw base read counts for each of the 4091 ORFs for all the 15 samples, and the explanation key is included in the file. PGCGROWTHCONDITIONS
Viable clones of the UvsW-expressing strains GJ13531 (Δrho) and GJ13507 (ΔnusG) were obtained as white colonies from their respective shelter plasmid-carrying derivatives GJ13531/pHYD2411 and GJ13507 /pHYD2412 on glucose-minimal A plates supplemented with Xgal and IPTG at 200 μM (for Δrho) or 3 μM (for ΔnusG), as previously described PGCGROWTHCONDITIONS
WT UvsW_replicate1 PGCGROWTHCONDITIONS
Aligned reads were designated to top and bottom strands using Samtools PGCGROWTHCONDITIONS
At the appropriate optical density, culture growth was instantaneously arrested by addition of an equal volume of chilled 100% ethanol, and the cells were stored at –80°C until they were processed for RNA extraction. The cells were lysed and total RNA was prepared by the hot phenol method essentially as described, after chromosomal DNA has been digested with RNase-free DNase. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
bcl2fastq2 v2.15.0 (Demultiplexing), Fastqc 0.11.5 (read quality), Cutadapt-1.9.1 (adaptor trimming) PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genome_build: NC000913.2 MG1655 PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
Reads were aligned using MG15655 as reference genome (NC000913.2) using Bowtie2 tool. PGCGROWTHCONDITIONS
ssRNA-seq PGCGROWTHCONDITIONS
Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS
Strand specific base read counts were determined for each of 4091 ORFs for the 15 samples PGCGROWTHCONDITIONS
Strand-specific RNA-Seq data were generated, following rRNA depletion with a Ribo-Zero kit, with the aid of the di-tagged cDNA strategy (ScriptSeq) on an Illumina NextSeq platform PGCGROWTHCONDITIONS
substrain: GJ13533 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The text file contains sense and antisense raw base read counts for each of the 4091 ORFs for all the 15 samples, and the explanation key is included in the file. PGCGROWTHCONDITIONS
Viable clones of the UvsW-expressing strains GJ13531 (Δrho) and GJ13507 (ΔnusG) were obtained as white colonies from their respective shelter plasmid-carrying derivatives GJ13531/pHYD2411 and GJ13507 /pHYD2412 on glucose-minimal A plates supplemented with Xgal and IPTG at 200 μM (for Δrho) or 3 μM (for ΔnusG), as previously described PGCGROWTHCONDITIONS
WT UvsW_replicate2 PGCGROWTHCONDITIONS
Aligned reads were designated to top and bottom strands using Samtools PGCGROWTHCONDITIONS
At the appropriate optical density, culture growth was instantaneously arrested by addition of an equal volume of chilled 100% ethanol, and the cells were stored at –80°C until they were processed for RNA extraction. The cells were lysed and total RNA was prepared by the hot phenol method essentially as described, after chromosomal DNA has been digested with RNase-free DNase. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
bcl2fastq2 v2.15.0 (Demultiplexing), Fastqc 0.11.5 (read quality), Cutadapt-1.9.1 (adaptor trimming) PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genome_build: NC000913.2 MG1655 PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
Reads were aligned using MG15655 as reference genome (NC000913.2) using Bowtie2 tool. PGCGROWTHCONDITIONS
ssRNA-seq PGCGROWTHCONDITIONS
Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS
Strand specific base read counts were determined for each of 4091 ORFs for the 15 samples PGCGROWTHCONDITIONS
Strand-specific RNA-Seq data were generated, following rRNA depletion with a Ribo-Zero kit, with the aid of the di-tagged cDNA strategy (ScriptSeq) on an Illumina NextSeq platform PGCGROWTHCONDITIONS
substrain: GJ13533 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The text file contains sense and antisense raw base read counts for each of the 4091 ORFs for all the 15 samples, and the explanation key is included in the file. PGCGROWTHCONDITIONS
Viable clones of the UvsW-expressing strains GJ13531 (Δrho) and GJ13507 (ΔnusG) were obtained as white colonies from their respective shelter plasmid-carrying derivatives GJ13531/pHYD2411 and GJ13507 /pHYD2412 on glucose-minimal A plates supplemented with Xgal and IPTG at 200 μM (for Δrho) or 3 μM (for ΔnusG), as previously described PGCGROWTHCONDITIONS
WT UvsW_replicate3 PGCGROWTHCONDITIONS
Aligned reads were designated to top and bottom strands using Samtools PGCGROWTHCONDITIONS
At the appropriate optical density, culture growth was instantaneously arrested by addition of an equal volume of chilled 100% ethanol, and the cells were stored at –80°C until they were processed for RNA extraction. The cells were lysed and total RNA was prepared by the hot phenol method essentially as described, after chromosomal DNA has been digested with RNase-free DNase. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
bcl2fastq2 v2.15.0 (Demultiplexing), Fastqc 0.11.5 (read quality), Cutadapt-1.9.1 (adaptor trimming) PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genome_build: NC000913.2 MG1655 PGCGROWTHCONDITIONS
genotype: {delta}rho PGCGROWTHCONDITIONS
Reads were aligned using MG15655 as reference genome (NC000913.2) using Bowtie2 tool. PGCGROWTHCONDITIONS
∆rho UvsW_replicate1 PGCGROWTHCONDITIONS
ssRNA-seq PGCGROWTHCONDITIONS
Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS
Strand specific base read counts were determined for each of 4091 ORFs for the 15 samples PGCGROWTHCONDITIONS
Strand-specific RNA-Seq data were generated, following rRNA depletion with a Ribo-Zero kit, with the aid of the di-tagged cDNA strategy (ScriptSeq) on an Illumina NextSeq platform PGCGROWTHCONDITIONS
substrain: GJ13531 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The text file contains sense and antisense raw base read counts for each of the 4091 ORFs for all the 15 samples, and the explanation key is included in the file. PGCGROWTHCONDITIONS
Viable clones of the UvsW-expressing strains GJ13531 (Δrho) and GJ13507 (ΔnusG) were obtained as white colonies from their respective shelter plasmid-carrying derivatives GJ13531/pHYD2411 and GJ13507 /pHYD2412 on glucose-minimal A plates supplemented with Xgal and IPTG at 200 μM (for Δrho) or 3 μM (for ΔnusG), as previously described PGCGROWTHCONDITIONS
Aligned reads were designated to top and bottom strands using Samtools PGCGROWTHCONDITIONS
At the appropriate optical density, culture growth was instantaneously arrested by addition of an equal volume of chilled 100% ethanol, and the cells were stored at –80°C until they were processed for RNA extraction. The cells were lysed and total RNA was prepared by the hot phenol method essentially as described, after chromosomal DNA has been digested with RNase-free DNase. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
bcl2fastq2 v2.15.0 (Demultiplexing), Fastqc 0.11.5 (read quality), Cutadapt-1.9.1 (adaptor trimming) PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genome_build: NC000913.2 MG1655 PGCGROWTHCONDITIONS
genotype: {delta}rho PGCGROWTHCONDITIONS
Reads were aligned using MG15655 as reference genome (NC000913.2) using Bowtie2 tool. PGCGROWTHCONDITIONS
∆rho UvsW_replicate2 PGCGROWTHCONDITIONS
ssRNA-seq PGCGROWTHCONDITIONS
Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS
Strand specific base read counts were determined for each of 4091 ORFs for the 15 samples PGCGROWTHCONDITIONS
Strand-specific RNA-Seq data were generated, following rRNA depletion with a Ribo-Zero kit, with the aid of the di-tagged cDNA strategy (ScriptSeq) on an Illumina NextSeq platform PGCGROWTHCONDITIONS
substrain: GJ13531 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The text file contains sense and antisense raw base read counts for each of the 4091 ORFs for all the 15 samples, and the explanation key is included in the file. PGCGROWTHCONDITIONS
Viable clones of the UvsW-expressing strains GJ13531 (Δrho) and GJ13507 (ΔnusG) were obtained as white colonies from their respective shelter plasmid-carrying derivatives GJ13531/pHYD2411 and GJ13507 /pHYD2412 on glucose-minimal A plates supplemented with Xgal and IPTG at 200 μM (for Δrho) or 3 μM (for ΔnusG), as previously described PGCGROWTHCONDITIONS
Aligned reads were designated to top and bottom strands using Samtools PGCGROWTHCONDITIONS
At the appropriate optical density, culture growth was instantaneously arrested by addition of an equal volume of chilled 100% ethanol, and the cells were stored at –80°C until they were processed for RNA extraction. The cells were lysed and total RNA was prepared by the hot phenol method essentially as described, after chromosomal DNA has been digested with RNase-free DNase. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
bcl2fastq2 v2.15.0 (Demultiplexing), Fastqc 0.11.5 (read quality), Cutadapt-1.9.1 (adaptor trimming) PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genome_build: NC000913.2 MG1655 PGCGROWTHCONDITIONS
genotype: {delta}rho PGCGROWTHCONDITIONS
Reads were aligned using MG15655 as reference genome (NC000913.2) using Bowtie2 tool. PGCGROWTHCONDITIONS
∆rho UvsW_replicate3 PGCGROWTHCONDITIONS
ssRNA-seq PGCGROWTHCONDITIONS
Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS
Strand specific base read counts were determined for each of 4091 ORFs for the 15 samples PGCGROWTHCONDITIONS
Strand-specific RNA-Seq data were generated, following rRNA depletion with a Ribo-Zero kit, with the aid of the di-tagged cDNA strategy (ScriptSeq) on an Illumina NextSeq platform PGCGROWTHCONDITIONS
substrain: GJ13531 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The text file contains sense and antisense raw base read counts for each of the 4091 ORFs for all the 15 samples, and the explanation key is included in the file. PGCGROWTHCONDITIONS
Viable clones of the UvsW-expressing strains GJ13531 (Δrho) and GJ13507 (ΔnusG) were obtained as white colonies from their respective shelter plasmid-carrying derivatives GJ13531/pHYD2411 and GJ13507 /pHYD2412 on glucose-minimal A plates supplemented with Xgal and IPTG at 200 μM (for Δrho) or 3 μM (for ΔnusG), as previously described PGCGROWTHCONDITIONS
Aligned reads were designated to top and bottom strands using Samtools PGCGROWTHCONDITIONS
At the appropriate optical density, culture growth was instantaneously arrested by addition of an equal volume of chilled 100% ethanol, and the cells were stored at –80°C until they were processed for RNA extraction. The cells were lysed and total RNA was prepared by the hot phenol method essentially as described, after chromosomal DNA has been digested with RNase-free DNase. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
bcl2fastq2 v2.15.0 (Demultiplexing), Fastqc 0.11.5 (read quality), Cutadapt-1.9.1 (adaptor trimming) PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genome_build: NC000913.2 MG1655 PGCGROWTHCONDITIONS
genotype: {delta}nusG PGCGROWTHCONDITIONS
∆nusG UvsW_replicate1 PGCGROWTHCONDITIONS
Reads were aligned using MG15655 as reference genome (NC000913.2) using Bowtie2 tool. PGCGROWTHCONDITIONS
ssRNA-seq PGCGROWTHCONDITIONS
Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS
Strand specific base read counts were determined for each of 4091 ORFs for the 15 samples PGCGROWTHCONDITIONS
Strand-specific RNA-Seq data were generated, following rRNA depletion with a Ribo-Zero kit, with the aid of the di-tagged cDNA strategy (ScriptSeq) on an Illumina NextSeq platform PGCGROWTHCONDITIONS
substrain: GJ13507 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The text file contains sense and antisense raw base read counts for each of the 4091 ORFs for all the 15 samples, and the explanation key is included in the file. PGCGROWTHCONDITIONS
Viable clones of the UvsW-expressing strains GJ13531 (Δrho) and GJ13507 (ΔnusG) were obtained as white colonies from their respective shelter plasmid-carrying derivatives GJ13531/pHYD2411 and GJ13507 /pHYD2412 on glucose-minimal A plates supplemented with Xgal and IPTG at 200 μM (for Δrho) or 3 μM (for ΔnusG), as previously described PGCGROWTHCONDITIONS
Aligned reads were designated to top and bottom strands using Samtools PGCGROWTHCONDITIONS
At the appropriate optical density, culture growth was instantaneously arrested by addition of an equal volume of chilled 100% ethanol, and the cells were stored at –80°C until they were processed for RNA extraction. The cells were lysed and total RNA was prepared by the hot phenol method essentially as described, after chromosomal DNA has been digested with RNase-free DNase. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
bcl2fastq2 v2.15.0 (Demultiplexing), Fastqc 0.11.5 (read quality), Cutadapt-1.9.1 (adaptor trimming) PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genome_build: NC000913.2 MG1655 PGCGROWTHCONDITIONS
genotype: {delta}nusG PGCGROWTHCONDITIONS
∆nusG UvsW_replicate2 PGCGROWTHCONDITIONS
Reads were aligned using MG15655 as reference genome (NC000913.2) using Bowtie2 tool. PGCGROWTHCONDITIONS
ssRNA-seq PGCGROWTHCONDITIONS
Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS
Strand specific base read counts were determined for each of 4091 ORFs for the 15 samples PGCGROWTHCONDITIONS
Strand-specific RNA-Seq data were generated, following rRNA depletion with a Ribo-Zero kit, with the aid of the di-tagged cDNA strategy (ScriptSeq) on an Illumina NextSeq platform PGCGROWTHCONDITIONS
substrain: GJ13507 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The text file contains sense and antisense raw base read counts for each of the 4091 ORFs for all the 15 samples, and the explanation key is included in the file. PGCGROWTHCONDITIONS
Viable clones of the UvsW-expressing strains GJ13531 (Δrho) and GJ13507 (ΔnusG) were obtained as white colonies from their respective shelter plasmid-carrying derivatives GJ13531/pHYD2411 and GJ13507 /pHYD2412 on glucose-minimal A plates supplemented with Xgal and IPTG at 200 μM (for Δrho) or 3 μM (for ΔnusG), as previously described PGCGROWTHCONDITIONS
Aligned reads were designated to top and bottom strands using Samtools PGCGROWTHCONDITIONS
At the appropriate optical density, culture growth was instantaneously arrested by addition of an equal volume of chilled 100% ethanol, and the cells were stored at –80°C until they were processed for RNA extraction. The cells were lysed and total RNA was prepared by the hot phenol method essentially as described, after chromosomal DNA has been digested with RNase-free DNase. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
bcl2fastq2 v2.15.0 (Demultiplexing), Fastqc 0.11.5 (read quality), Cutadapt-1.9.1 (adaptor trimming) PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genome_build: NC000913.2 MG1655 PGCGROWTHCONDITIONS
genotype: {delta}nusG PGCGROWTHCONDITIONS
∆nusG UvsW_replicate3 PGCGROWTHCONDITIONS
Reads were aligned using MG15655 as reference genome (NC000913.2) using Bowtie2 tool. PGCGROWTHCONDITIONS
ssRNA-seq PGCGROWTHCONDITIONS
Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS
Strand specific base read counts were determined for each of 4091 ORFs for the 15 samples PGCGROWTHCONDITIONS
Strand-specific RNA-Seq data were generated, following rRNA depletion with a Ribo-Zero kit, with the aid of the di-tagged cDNA strategy (ScriptSeq) on an Illumina NextSeq platform PGCGROWTHCONDITIONS
substrain: GJ13507 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The text file contains sense and antisense raw base read counts for each of the 4091 ORFs for all the 15 samples, and the explanation key is included in the file. PGCGROWTHCONDITIONS
Viable clones of the UvsW-expressing strains GJ13531 (Δrho) and GJ13507 (ΔnusG) were obtained as white colonies from their respective shelter plasmid-carrying derivatives GJ13531/pHYD2411 and GJ13507 /pHYD2412 on glucose-minimal A plates supplemented with Xgal and IPTG at 200 μM (for Δrho) or 3 μM (for ΔnusG), as previously described PGCGROWTHCONDITIONS
cells PGCGROWTHCONDITIONS
Cells were inoculated from overnight grown culture in Lysogeny Broth (LB) and then harvested in the early exponential growth phase and mid exponential growth phase. PGCGROWTHCONDITIONS
crp.rep1.ee PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (NC000913.2) PGCGROWTHCONDITIONS
genotype: crp mutant background PGCGROWTHCONDITIONS
growth phase: Early exponential PGCGROWTHCONDITIONS
NEXTflexRapid Directional RNA-Seq library kit PGCGROWTHCONDITIONS
Raw .fastq files were mapped to the reference genome (NC000913.2) using BWA (version 0.7). Mapped reads were then converted to read count per gene using bedtools (version 2).  In the case of Ion torrent data .bam files were converted using BWA. PGCGROWTHCONDITIONS
Resulting read count matrix was used as input for the differntial expression analysis in edgeR (version 3.12.1). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from the harvested cells using Trizol reagent. Depending upon the concentration of total RNA, sample were treated with Dnase and ribocleanup was given according to the instruction manual. PGCGROWTHCONDITIONS
srain: K12 MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .txt (log2 fold change values, p-values) PGCGROWTHCONDITIONS
cells PGCGROWTHCONDITIONS
Cells were inoculated from overnight grown culture in Lysogeny Broth (LB) and then harvested in the early exponential growth phase and mid exponential growth phase. PGCGROWTHCONDITIONS
crp.rep2.ee PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (NC000913.2) PGCGROWTHCONDITIONS
genotype: crp mutant background PGCGROWTHCONDITIONS
growth phase: Early exponential PGCGROWTHCONDITIONS
NEXTflexRapid Directional RNA-Seq library kit PGCGROWTHCONDITIONS
Raw .fastq files were mapped to the reference genome (NC000913.2) using BWA (version 0.7). Mapped reads were then converted to read count per gene using bedtools (version 2).  In the case of Ion torrent data .bam files were converted using BWA. PGCGROWTHCONDITIONS
Resulting read count matrix was used as input for the differntial expression analysis in edgeR (version 3.12.1). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from the harvested cells using Trizol reagent. Depending upon the concentration of total RNA, sample were treated with Dnase and ribocleanup was given according to the instruction manual. PGCGROWTHCONDITIONS
srain: K12 MG1656 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .txt (log2 fold change values, p-values) PGCGROWTHCONDITIONS
cells PGCGROWTHCONDITIONS
Cells were inoculated from overnight grown culture in Lysogeny Broth (LB) and then harvested in the early exponential growth phase and mid exponential growth phase. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
fis.rep1.ee PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (NC000913.2) PGCGROWTHCONDITIONS
genotype: fis mutant background PGCGROWTHCONDITIONS
growth phase: Early exponential PGCGROWTHCONDITIONS
NEXTflexRapid Directional RNA-Seq library kit PGCGROWTHCONDITIONS
Raw .fastq files were mapped to the reference genome (NC000913.2) using BWA (version 0.7). Mapped reads were then converted to read count per gene using bedtools (version 2).  In the case of Ion torrent data .bam files were converted using BWA. PGCGROWTHCONDITIONS
Resulting read count matrix was used as input for the differntial expression analysis in edgeR (version 3.12.1). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from the harvested cells using Trizol reagent. Depending upon the concentration of total RNA, sample were treated with Dnase and ribocleanup was given according to the instruction manual. PGCGROWTHCONDITIONS
srain: K12 MG1657 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .txt (log2 fold change values, p-values) PGCGROWTHCONDITIONS
cells PGCGROWTHCONDITIONS
Cells were inoculated from overnight grown culture in Lysogeny Broth (LB) and then harvested in the early exponential growth phase and mid exponential growth phase. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
fis.rep2.ee PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (NC000913.2) PGCGROWTHCONDITIONS
genotype: fis mutant background PGCGROWTHCONDITIONS
growth phase: Early exponential PGCGROWTHCONDITIONS
NEXTflexRapid Directional RNA-Seq library kit PGCGROWTHCONDITIONS
Raw .fastq files were mapped to the reference genome (NC000913.2) using BWA (version 0.7). Mapped reads were then converted to read count per gene using bedtools (version 2).  In the case of Ion torrent data .bam files were converted using BWA. PGCGROWTHCONDITIONS
Resulting read count matrix was used as input for the differntial expression analysis in edgeR (version 3.12.1). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from the harvested cells using Trizol reagent. Depending upon the concentration of total RNA, sample were treated with Dnase and ribocleanup was given according to the instruction manual. PGCGROWTHCONDITIONS
srain: K12 MG1658 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .txt (log2 fold change values, p-values) PGCGROWTHCONDITIONS
cells PGCGROWTHCONDITIONS
Cells were inoculated from overnight grown culture in Lysogeny Broth (LB) and then harvested in the early exponential growth phase and mid exponential growth phase. PGCGROWTHCONDITIONS
crpfis.rep1.ee PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (NC000913.2) PGCGROWTHCONDITIONS
genotype: crpfis mutant background PGCGROWTHCONDITIONS
growth phase: Early exponential PGCGROWTHCONDITIONS
NEXTflexRapid Directional RNA-Seq library kit PGCGROWTHCONDITIONS
Raw .fastq files were mapped to the reference genome (NC000913.2) using BWA (version 0.7). Mapped reads were then converted to read count per gene using bedtools (version 2).  In the case of Ion torrent data .bam files were converted using BWA. PGCGROWTHCONDITIONS
Resulting read count matrix was used as input for the differntial expression analysis in edgeR (version 3.12.1). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from the harvested cells using Trizol reagent. Depending upon the concentration of total RNA, sample were treated with Dnase and ribocleanup was given according to the instruction manual. PGCGROWTHCONDITIONS
srain: K12 MG1659 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .txt (log2 fold change values, p-values) PGCGROWTHCONDITIONS
cells PGCGROWTHCONDITIONS
Cells were inoculated from overnight grown culture in Lysogeny Broth (LB) and then harvested in the early exponential growth phase and mid exponential growth phase. PGCGROWTHCONDITIONS
crpfis.rep2.ee PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (NC000913.2) PGCGROWTHCONDITIONS
genotype: crpfis mutant background PGCGROWTHCONDITIONS
growth phase: Early exponential PGCGROWTHCONDITIONS
NEXTflexRapid Directional RNA-Seq library kit PGCGROWTHCONDITIONS
Raw .fastq files were mapped to the reference genome (NC000913.2) using BWA (version 0.7). Mapped reads were then converted to read count per gene using bedtools (version 2).  In the case of Ion torrent data .bam files were converted using BWA. PGCGROWTHCONDITIONS
Resulting read count matrix was used as input for the differntial expression analysis in edgeR (version 3.12.1). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from the harvested cells using Trizol reagent. Depending upon the concentration of total RNA, sample were treated with Dnase and ribocleanup was given according to the instruction manual. PGCGROWTHCONDITIONS
srain: K12 MG1660 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .txt (log2 fold change values, p-values) PGCGROWTHCONDITIONS
cells PGCGROWTHCONDITIONS
Cells were inoculated from overnight grown culture in Lysogeny Broth (LB) and then harvested in the early exponential growth phase and mid exponential growth phase. PGCGROWTHCONDITIONS
cya.rep1.ee PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (NC000913.2) PGCGROWTHCONDITIONS
genotype: cya mutant background PGCGROWTHCONDITIONS
growth phase: Early exponential PGCGROWTHCONDITIONS
NEXTflexRapid Directional RNA-Seq library kit PGCGROWTHCONDITIONS
Raw .fastq files were mapped to the reference genome (NC000913.2) using BWA (version 0.7). Mapped reads were then converted to read count per gene using bedtools (version 2).  In the case of Ion torrent data .bam files were converted using BWA. PGCGROWTHCONDITIONS
Resulting read count matrix was used as input for the differntial expression analysis in edgeR (version 3.12.1). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from the harvested cells using Trizol reagent. Depending upon the concentration of total RNA, sample were treated with Dnase and ribocleanup was given according to the instruction manual. PGCGROWTHCONDITIONS
srain: K12 MG1661 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .txt (log2 fold change values, p-values) PGCGROWTHCONDITIONS
cells PGCGROWTHCONDITIONS
Cells were inoculated from overnight grown culture in Lysogeny Broth (LB) and then harvested in the early exponential growth phase and mid exponential growth phase. PGCGROWTHCONDITIONS
cya.rep2.ee PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (NC000913.2) PGCGROWTHCONDITIONS
genotype: cya mutant background PGCGROWTHCONDITIONS
growth phase: Early exponential PGCGROWTHCONDITIONS
NEXTflexRapid Directional RNA-Seq library kit PGCGROWTHCONDITIONS
Raw .fastq files were mapped to the reference genome (NC000913.2) using BWA (version 0.7). Mapped reads were then converted to read count per gene using bedtools (version 2).  In the case of Ion torrent data .bam files were converted using BWA. PGCGROWTHCONDITIONS
Resulting read count matrix was used as input for the differntial expression analysis in edgeR (version 3.12.1). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from the harvested cells using Trizol reagent. Depending upon the concentration of total RNA, sample were treated with Dnase and ribocleanup was given according to the instruction manual. PGCGROWTHCONDITIONS
srain: K12 MG1662 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .txt (log2 fold change values, p-values) PGCGROWTHCONDITIONS
cells PGCGROWTHCONDITIONS
Cells were inoculated from overnight grown culture in Lysogeny Broth (LB) and then harvested in the early exponential growth phase and mid exponential growth phase. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (NC000913.2) PGCGROWTHCONDITIONS
genotype: wildtype PGCGROWTHCONDITIONS
growth phase: Early exponential PGCGROWTHCONDITIONS
NEXTflexRapid Directional RNA-Seq library kit PGCGROWTHCONDITIONS
Raw .fastq files were mapped to the reference genome (NC000913.2) using BWA (version 0.7). Mapped reads were then converted to read count per gene using bedtools (version 2).  In the case of Ion torrent data .bam files were converted using BWA. PGCGROWTHCONDITIONS
Resulting read count matrix was used as input for the differntial expression analysis in edgeR (version 3.12.1). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from the harvested cells using Trizol reagent. Depending upon the concentration of total RNA, sample were treated with Dnase and ribocleanup was given according to the instruction manual. PGCGROWTHCONDITIONS
srain: K12 MG1663 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .txt (log2 fold change values, p-values) PGCGROWTHCONDITIONS
wt.rep1.ee PGCGROWTHCONDITIONS
cells PGCGROWTHCONDITIONS
Cells were inoculated from overnight grown culture in Lysogeny Broth (LB) and then harvested in the early exponential growth phase and mid exponential growth phase. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (NC000913.2) PGCGROWTHCONDITIONS
genotype: wildtype PGCGROWTHCONDITIONS
growth phase: Early exponential PGCGROWTHCONDITIONS
NEXTflexRapid Directional RNA-Seq library kit PGCGROWTHCONDITIONS
Raw .fastq files were mapped to the reference genome (NC000913.2) using BWA (version 0.7). Mapped reads were then converted to read count per gene using bedtools (version 2).  In the case of Ion torrent data .bam files were converted using BWA. PGCGROWTHCONDITIONS
Resulting read count matrix was used as input for the differntial expression analysis in edgeR (version 3.12.1). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from the harvested cells using Trizol reagent. Depending upon the concentration of total RNA, sample were treated with Dnase and ribocleanup was given according to the instruction manual. PGCGROWTHCONDITIONS
srain: K12 MG1664 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .txt (log2 fold change values, p-values) PGCGROWTHCONDITIONS
wt.rep2.ee PGCGROWTHCONDITIONS
cells PGCGROWTHCONDITIONS
Cells were inoculated from overnight grown culture in Lysogeny Broth (LB) and then harvested in the early exponential growth phase and mid exponential growth phase. PGCGROWTHCONDITIONS
crp.rep1.me PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (NC000913.2) PGCGROWTHCONDITIONS
genotype: crp mutant background PGCGROWTHCONDITIONS
growth phase: Mid exponential PGCGROWTHCONDITIONS
NEXTflexRapid Directional RNA-Seq library kit PGCGROWTHCONDITIONS
Raw .fastq files were mapped to the reference genome (NC000913.2) using BWA (version 0.7). Mapped reads were then converted to read count per gene using bedtools (version 2).  In the case of Ion torrent data .bam files were converted using BWA. PGCGROWTHCONDITIONS
Resulting read count matrix was used as input for the differntial expression analysis in edgeR (version 3.12.1). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from the harvested cells using Trizol reagent. Depending upon the concentration of total RNA, sample were treated with Dnase and ribocleanup was given according to the instruction manual. PGCGROWTHCONDITIONS
srain: K12 MG1665 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .txt (log2 fold change values, p-values) PGCGROWTHCONDITIONS
cells PGCGROWTHCONDITIONS
Cells were inoculated from overnight grown culture in Lysogeny Broth (LB) and then harvested in the early exponential growth phase and mid exponential growth phase. PGCGROWTHCONDITIONS
crp.rep2.me PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (NC000913.2) PGCGROWTHCONDITIONS
genotype: crp mutant background PGCGROWTHCONDITIONS
growth phase: Mid exponential PGCGROWTHCONDITIONS
NEXTflexRapid Directional RNA-Seq library kit PGCGROWTHCONDITIONS
Raw .fastq files were mapped to the reference genome (NC000913.2) using BWA (version 0.7). Mapped reads were then converted to read count per gene using bedtools (version 2).  In the case of Ion torrent data .bam files were converted using BWA. PGCGROWTHCONDITIONS
Resulting read count matrix was used as input for the differntial expression analysis in edgeR (version 3.12.1). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from the harvested cells using Trizol reagent. Depending upon the concentration of total RNA, sample were treated with Dnase and ribocleanup was given according to the instruction manual. PGCGROWTHCONDITIONS
srain: K12 MG1666 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .txt (log2 fold change values, p-values) PGCGROWTHCONDITIONS
cells PGCGROWTHCONDITIONS
Cells were inoculated from overnight grown culture in Lysogeny Broth (LB) and then harvested in the early exponential growth phase and mid exponential growth phase. PGCGROWTHCONDITIONS
crpfis.rep1.me PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (NC000913.2) PGCGROWTHCONDITIONS
genotype: crpfis mutant background PGCGROWTHCONDITIONS
growth phase: Mid exponential PGCGROWTHCONDITIONS
NEXTflexRapid Directional RNA-Seq library kit PGCGROWTHCONDITIONS
Raw .fastq files were mapped to the reference genome (NC000913.2) using BWA (version 0.7). Mapped reads were then converted to read count per gene using bedtools (version 2).  In the case of Ion torrent data .bam files were converted using BWA. PGCGROWTHCONDITIONS
Resulting read count matrix was used as input for the differntial expression analysis in edgeR (version 3.12.1). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from the harvested cells using Trizol reagent. Depending upon the concentration of total RNA, sample were treated with Dnase and ribocleanup was given according to the instruction manual. PGCGROWTHCONDITIONS
srain: K12 MG1669 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .txt (log2 fold change values, p-values) PGCGROWTHCONDITIONS
cells PGCGROWTHCONDITIONS
Cells were inoculated from overnight grown culture in Lysogeny Broth (LB) and then harvested in the early exponential growth phase and mid exponential growth phase. PGCGROWTHCONDITIONS
crpfis.rep2.me PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (NC000913.2) PGCGROWTHCONDITIONS
genotype: crpfis mutant background PGCGROWTHCONDITIONS
growth phase: Mid exponential PGCGROWTHCONDITIONS
NEXTflexRapid Directional RNA-Seq library kit PGCGROWTHCONDITIONS
Raw .fastq files were mapped to the reference genome (NC000913.2) using BWA (version 0.7). Mapped reads were then converted to read count per gene using bedtools (version 2).  In the case of Ion torrent data .bam files were converted using BWA. PGCGROWTHCONDITIONS
Resulting read count matrix was used as input for the differntial expression analysis in edgeR (version 3.12.1). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from the harvested cells using Trizol reagent. Depending upon the concentration of total RNA, sample were treated with Dnase and ribocleanup was given according to the instruction manual. PGCGROWTHCONDITIONS
srain: K12 MG1670 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .txt (log2 fold change values, p-values) PGCGROWTHCONDITIONS
cells PGCGROWTHCONDITIONS
Cells were inoculated from overnight grown culture in Lysogeny Broth (LB) and then harvested in the early exponential growth phase and mid exponential growth phase. PGCGROWTHCONDITIONS
cya.rep1.me PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (NC000913.2) PGCGROWTHCONDITIONS
genotype: cya mutant background PGCGROWTHCONDITIONS
growth phase: Mid exponential PGCGROWTHCONDITIONS
NEXTflexRapid Directional RNA-Seq library kit PGCGROWTHCONDITIONS
Raw .fastq files were mapped to the reference genome (NC000913.2) using BWA (version 0.7). Mapped reads were then converted to read count per gene using bedtools (version 2).  In the case of Ion torrent data .bam files were converted using BWA. PGCGROWTHCONDITIONS
Resulting read count matrix was used as input for the differntial expression analysis in edgeR (version 3.12.1). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from the harvested cells using Trizol reagent. Depending upon the concentration of total RNA, sample were treated with Dnase and ribocleanup was given according to the instruction manual. PGCGROWTHCONDITIONS
srain: K12 MG1671 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .txt (log2 fold change values, p-values) PGCGROWTHCONDITIONS
cells PGCGROWTHCONDITIONS
Cells were inoculated from overnight grown culture in Lysogeny Broth (LB) and then harvested in the early exponential growth phase and mid exponential growth phase. PGCGROWTHCONDITIONS
cya.rep2.me PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (NC000913.2) PGCGROWTHCONDITIONS
genotype: cya mutant background PGCGROWTHCONDITIONS
growth phase: Mid exponential PGCGROWTHCONDITIONS
NEXTflexRapid Directional RNA-Seq library kit PGCGROWTHCONDITIONS
Raw .fastq files were mapped to the reference genome (NC000913.2) using BWA (version 0.7). Mapped reads were then converted to read count per gene using bedtools (version 2).  In the case of Ion torrent data .bam files were converted using BWA. PGCGROWTHCONDITIONS
Resulting read count matrix was used as input for the differntial expression analysis in edgeR (version 3.12.1). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from the harvested cells using Trizol reagent. Depending upon the concentration of total RNA, sample were treated with Dnase and ribocleanup was given according to the instruction manual. PGCGROWTHCONDITIONS
srain: K12 MG1672 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .txt (log2 fold change values, p-values) PGCGROWTHCONDITIONS
cells PGCGROWTHCONDITIONS
Cells were inoculated from overnight grown culture in Lysogeny Broth (LB) and then harvested in the early exponential growth phase and mid exponential growth phase. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (NC000913.2) PGCGROWTHCONDITIONS
genotype: wildtype PGCGROWTHCONDITIONS
growth phase: Mid exponential PGCGROWTHCONDITIONS
NEXTflexRapid Directional RNA-Seq library kit PGCGROWTHCONDITIONS
Raw .fastq files were mapped to the reference genome (NC000913.2) using BWA (version 0.7). Mapped reads were then converted to read count per gene using bedtools (version 2).  In the case of Ion torrent data .bam files were converted using BWA. PGCGROWTHCONDITIONS
Resulting read count matrix was used as input for the differntial expression analysis in edgeR (version 3.12.1). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from the harvested cells using Trizol reagent. Depending upon the concentration of total RNA, sample were treated with Dnase and ribocleanup was given according to the instruction manual. PGCGROWTHCONDITIONS
srain: K12 MG1673 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .txt (log2 fold change values, p-values) PGCGROWTHCONDITIONS
wt.rep1.me PGCGROWTHCONDITIONS
cells PGCGROWTHCONDITIONS
Cells were inoculated from overnight grown culture in Lysogeny Broth (LB) and then harvested in the early exponential growth phase and mid exponential growth phase. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (NC000913.2) PGCGROWTHCONDITIONS
genotype: wildtype PGCGROWTHCONDITIONS
growth phase: Mid exponential PGCGROWTHCONDITIONS
NEXTflexRapid Directional RNA-Seq library kit PGCGROWTHCONDITIONS
Raw .fastq files were mapped to the reference genome (NC000913.2) using BWA (version 0.7). Mapped reads were then converted to read count per gene using bedtools (version 2).  In the case of Ion torrent data .bam files were converted using BWA. PGCGROWTHCONDITIONS
Resulting read count matrix was used as input for the differntial expression analysis in edgeR (version 3.12.1). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from the harvested cells using Trizol reagent. Depending upon the concentration of total RNA, sample were treated with Dnase and ribocleanup was given according to the instruction manual. PGCGROWTHCONDITIONS
srain: K12 MG1674 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: .txt (log2 fold change values, p-values) PGCGROWTHCONDITIONS
wt.rep2.me PGCGROWTHCONDITIONS
cell pellets PGCGROWTHCONDITIONS
E. coli 042 WT PGCGROWTHCONDITIONS
Escherichia coli 042 PGCGROWTHCONDITIONS
For quantification of gene expression (read counting), the alignments generated with the Genomics Workbench were exported in BAM format. Read counting was then performed with the FeatureCounts v. 1.5.0-p1 program using the following parameters; Level : meta-feature leve. Paired-end : no. Strand specific : yes. Multimapping reads : counted (as fractions). Multi-overlapping reads : not counted. Overlapping bases : 30. Read orientations : fr PGCGROWTHCONDITIONS
From the rRNA depleted RNA samples, first-strand cDNA was synthesized using a N6 randomized primer. After fragmentation, the Illumina TruSeq sequencing adapters were ligated in a strand specific manner to the 5' and 3' ends of the cDNA fragments. The cDNA was finally amplified with PCR (15 PCR cycles) using a proof reading enzyme. For Illumina sequencing, cDNA libraries were pooled in a 25:1 ratio. The library pool was fractionated in the size range of 250-500 bp using a differential clean- up with the Agencourt AMPure kit. The cDNA pool was sequenced on an Illumina NextSeq 500 system using 75 bp read length. PGCGROWTHCONDITIONS
Genome_build: NCBI reference sequence (NC_017626.1) PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
Illumina sequencing instruments generate per-cycle BCL base call files as primary sequencing output in bcl2 format. Conversion of the bcl2 file to gzipped fastq files was performed using the bcl2fastq script v. 2.18.0.12 provided by Illumina. PGCGROWTHCONDITIONS
LB medium at 37ºC with 200rpm agitation. PGCGROWTHCONDITIONS
Mapping of the trimmed reads to the reference sequences was also performed with the CLC Genomics Workbench 9.0 using the 'Map Reads to Reference' tool with standard parameters. PGCGROWTHCONDITIONS
Quality and adapter trimming was performed with the CLC Genomics Workbench 9.0 software package using the 'Trim Sequences' tool with standard parameters. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Strain-expression.xlsx archive contains expression values in RPKM (Reads Per Kb exon (contig) per Million mapped  reads ( see Mortazavi et al. 2008, Nat Methods. 5(7):621-8 ) and can be directly compared to each other)  tab-delimited text files include RPKM values for each Sample. PGCGROWTHCONDITIONS
Total RNA was isolated from the cell pellets using a bead mill and the mirVana RNA isolation kit (Ambion) including DNase treatment. From the total RNA samples, ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Removal Kit for bacteria (Illumina). PGCGROWTHCONDITIONS
We used an Illumina NextSeq 500 system and a MID 150 Kit with 1x75 bp read length. Base-calling was perform online during the sequencing procedure with the Real-Time Analysis (RTA) software version 2.4.11 and System Suite Version 2.1.2.1. PGCGROWTHCONDITIONS
cell pellets PGCGROWTHCONDITIONS
E. coli hhahha2 PGCGROWTHCONDITIONS
Escherichia coli 042 PGCGROWTHCONDITIONS
For quantification of gene expression (read counting), the alignments generated with the Genomics Workbench were exported in BAM format. Read counting was then performed with the FeatureCounts v. 1.5.0-p1 program using the following parameters; Level : meta-feature leve. Paired-end : no. Strand specific : yes. Multimapping reads : counted (as fractions). Multi-overlapping reads : not counted. Overlapping bases : 30. Read orientations : fr PGCGROWTHCONDITIONS
From the rRNA depleted RNA samples, first-strand cDNA was synthesized using a N6 randomized primer. After fragmentation, the Illumina TruSeq sequencing adapters were ligated in a strand specific manner to the 5' and 3' ends of the cDNA fragments. The cDNA was finally amplified with PCR (15 PCR cycles) using a proof reading enzyme. For Illumina sequencing, cDNA libraries were pooled in a 25:1 ratio. The library pool was fractionated in the size range of 250-500 bp using a differential clean- up with the Agencourt AMPure kit. The cDNA pool was sequenced on an Illumina NextSeq 500 system using 75 bp read length. PGCGROWTHCONDITIONS
Genome_build: NCBI reference sequence (NC_017626.1) PGCGROWTHCONDITIONS
genotype: mutant hhahha2 PGCGROWTHCONDITIONS
Illumina sequencing instruments generate per-cycle BCL base call files as primary sequencing output in bcl2 format. Conversion of the bcl2 file to gzipped fastq files was performed using the bcl2fastq script v. 2.18.0.12 provided by Illumina. PGCGROWTHCONDITIONS
LB medium at 37ºC with 200rpm agitation. PGCGROWTHCONDITIONS
Mapping of the trimmed reads to the reference sequences was also performed with the CLC Genomics Workbench 9.0 using the 'Map Reads to Reference' tool with standard parameters. PGCGROWTHCONDITIONS
Quality and adapter trimming was performed with the CLC Genomics Workbench 9.0 software package using the 'Trim Sequences' tool with standard parameters. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Strain-expression.xlsx archive contains expression values in RPKM (Reads Per Kb exon (contig) per Million mapped  reads ( see Mortazavi et al. 2008, Nat Methods. 5(7):621-8 ) and can be directly compared to each other)  tab-delimited text files include RPKM values for each Sample. PGCGROWTHCONDITIONS
Total RNA was isolated from the cell pellets using a bead mill and the mirVana RNA isolation kit (Ambion) including DNase treatment. From the total RNA samples, ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Removal Kit for bacteria (Illumina). PGCGROWTHCONDITIONS
We used an Illumina NextSeq 500 system and a MID 150 Kit with 1x75 bp read length. Base-calling was perform online during the sequencing procedure with the Real-Time Analysis (RTA) software version 2.4.11 and System Suite Version 2.1.2.1. PGCGROWTHCONDITIONS
cell pellets PGCGROWTHCONDITIONS
E. coli hns PGCGROWTHCONDITIONS
Escherichia coli 042 PGCGROWTHCONDITIONS
For quantification of gene expression (read counting), the alignments generated with the Genomics Workbench were exported in BAM format. Read counting was then performed with the FeatureCounts v. 1.5.0-p1 program using the following parameters; Level : meta-feature leve. Paired-end : no. Strand specific : yes. Multimapping reads : counted (as fractions). Multi-overlapping reads : not counted. Overlapping bases : 30. Read orientations : fr PGCGROWTHCONDITIONS
From the rRNA depleted RNA samples, first-strand cDNA was synthesized using a N6 randomized primer. After fragmentation, the Illumina TruSeq sequencing adapters were ligated in a strand specific manner to the 5' and 3' ends of the cDNA fragments. The cDNA was finally amplified with PCR (15 PCR cycles) using a proof reading enzyme. For Illumina sequencing, cDNA libraries were pooled in a 25:1 ratio. The library pool was fractionated in the size range of 250-500 bp using a differential clean- up with the Agencourt AMPure kit. The cDNA pool was sequenced on an Illumina NextSeq 500 system using 75 bp read length. PGCGROWTHCONDITIONS
Genome_build: NCBI reference sequence (NC_017626.1) PGCGROWTHCONDITIONS
genotype: mutant hhs PGCGROWTHCONDITIONS
Illumina sequencing instruments generate per-cycle BCL base call files as primary sequencing output in bcl2 format. Conversion of the bcl2 file to gzipped fastq files was performed using the bcl2fastq script v. 2.18.0.12 provided by Illumina. PGCGROWTHCONDITIONS
LB medium at 37ºC with 200rpm agitation. PGCGROWTHCONDITIONS
Mapping of the trimmed reads to the reference sequences was also performed with the CLC Genomics Workbench 9.0 using the 'Map Reads to Reference' tool with standard parameters. PGCGROWTHCONDITIONS
Quality and adapter trimming was performed with the CLC Genomics Workbench 9.0 software package using the 'Trim Sequences' tool with standard parameters. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Strain-expression.xlsx archive contains expression values in RPKM (Reads Per Kb exon (contig) per Million mapped  reads ( see Mortazavi et al. 2008, Nat Methods. 5(7):621-8 ) and can be directly compared to each other)  tab-delimited text files include RPKM values for each Sample. PGCGROWTHCONDITIONS
Total RNA was isolated from the cell pellets using a bead mill and the mirVana RNA isolation kit (Ambion) including DNase treatment. From the total RNA samples, ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Removal Kit for bacteria (Illumina). PGCGROWTHCONDITIONS
We used an Illumina NextSeq 500 system and a MID 150 Kit with 1x75 bp read length. Base-calling was perform online during the sequencing procedure with the Real-Time Analysis (RTA) software version 2.4.11 and System Suite Version 2.1.2.1. PGCGROWTHCONDITIONS
cell pellets PGCGROWTHCONDITIONS
E. coli hns2 PGCGROWTHCONDITIONS
Escherichia coli 042 PGCGROWTHCONDITIONS
For quantification of gene expression (read counting), the alignments generated with the Genomics Workbench were exported in BAM format. Read counting was then performed with the FeatureCounts v. 1.5.0-p1 program using the following parameters; Level : meta-feature leve. Paired-end : no. Strand specific : yes. Multimapping reads : counted (as fractions). Multi-overlapping reads : not counted. Overlapping bases : 30. Read orientations : fr PGCGROWTHCONDITIONS
From the rRNA depleted RNA samples, first-strand cDNA was synthesized using a N6 randomized primer. After fragmentation, the Illumina TruSeq sequencing adapters were ligated in a strand specific manner to the 5' and 3' ends of the cDNA fragments. The cDNA was finally amplified with PCR (15 PCR cycles) using a proof reading enzyme. For Illumina sequencing, cDNA libraries were pooled in a 25:1 ratio. The library pool was fractionated in the size range of 250-500 bp using a differential clean- up with the Agencourt AMPure kit. The cDNA pool was sequenced on an Illumina NextSeq 500 system using 75 bp read length. PGCGROWTHCONDITIONS
Genome_build: NCBI reference sequence (NC_017626.1) PGCGROWTHCONDITIONS
genotype: mutant hns2 PGCGROWTHCONDITIONS
Illumina sequencing instruments generate per-cycle BCL base call files as primary sequencing output in bcl2 format. Conversion of the bcl2 file to gzipped fastq files was performed using the bcl2fastq script v. 2.18.0.12 provided by Illumina. PGCGROWTHCONDITIONS
LB medium at 37ºC with 200rpm agitation. PGCGROWTHCONDITIONS
Mapping of the trimmed reads to the reference sequences was also performed with the CLC Genomics Workbench 9.0 using the 'Map Reads to Reference' tool with standard parameters. PGCGROWTHCONDITIONS
Quality and adapter trimming was performed with the CLC Genomics Workbench 9.0 software package using the 'Trim Sequences' tool with standard parameters. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Strain-expression.xlsx archive contains expression values in RPKM (Reads Per Kb exon (contig) per Million mapped  reads ( see Mortazavi et al. 2008, Nat Methods. 5(7):621-8 ) and can be directly compared to each other)  tab-delimited text files include RPKM values for each Sample. PGCGROWTHCONDITIONS
Total RNA was isolated from the cell pellets using a bead mill and the mirVana RNA isolation kit (Ambion) including DNase treatment. From the total RNA samples, ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Removal Kit for bacteria (Illumina). PGCGROWTHCONDITIONS
We used an Illumina NextSeq 500 system and a MID 150 Kit with 1x75 bp read length. Base-calling was perform online during the sequencing procedure with the Real-Time Analysis (RTA) software version 2.4.11 and System Suite Version 2.1.2.1. PGCGROWTHCONDITIONS
cell pellets PGCGROWTHCONDITIONS
E. coli hnshns2 PGCGROWTHCONDITIONS
Escherichia coli 042 PGCGROWTHCONDITIONS
For quantification of gene expression (read counting), the alignments generated with the Genomics Workbench were exported in BAM format. Read counting was then performed with the FeatureCounts v. 1.5.0-p1 program using the following parameters; Level : meta-feature leve. Paired-end : no. Strand specific : yes. Multimapping reads : counted (as fractions). Multi-overlapping reads : not counted. Overlapping bases : 30. Read orientations : fr PGCGROWTHCONDITIONS
From the rRNA depleted RNA samples, first-strand cDNA was synthesized using a N6 randomized primer. After fragmentation, the Illumina TruSeq sequencing adapters were ligated in a strand specific manner to the 5' and 3' ends of the cDNA fragments. The cDNA was finally amplified with PCR (15 PCR cycles) using a proof reading enzyme. For Illumina sequencing, cDNA libraries were pooled in a 25:1 ratio. The library pool was fractionated in the size range of 250-500 bp using a differential clean- up with the Agencourt AMPure kit. The cDNA pool was sequenced on an Illumina NextSeq 500 system using 75 bp read length. PGCGROWTHCONDITIONS
Genome_build: NCBI reference sequence (NC_017626.1) PGCGROWTHCONDITIONS
genotype: mutant hnshns2 PGCGROWTHCONDITIONS
Illumina sequencing instruments generate per-cycle BCL base call files as primary sequencing output in bcl2 format. Conversion of the bcl2 file to gzipped fastq files was performed using the bcl2fastq script v. 2.18.0.12 provided by Illumina. PGCGROWTHCONDITIONS
LB medium at 37ºC with 200rpm agitation. PGCGROWTHCONDITIONS
Mapping of the trimmed reads to the reference sequences was also performed with the CLC Genomics Workbench 9.0 using the 'Map Reads to Reference' tool with standard parameters. PGCGROWTHCONDITIONS
Quality and adapter trimming was performed with the CLC Genomics Workbench 9.0 software package using the 'Trim Sequences' tool with standard parameters. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Strain-expression.xlsx archive contains expression values in RPKM (Reads Per Kb exon (contig) per Million mapped  reads ( see Mortazavi et al. 2008, Nat Methods. 5(7):621-8 ) and can be directly compared to each other)  tab-delimited text files include RPKM values for each Sample. PGCGROWTHCONDITIONS
Total RNA was isolated from the cell pellets using a bead mill and the mirVana RNA isolation kit (Ambion) including DNase treatment. From the total RNA samples, ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Removal Kit for bacteria (Illumina). PGCGROWTHCONDITIONS
We used an Illumina NextSeq 500 system and a MID 150 Kit with 1x75 bp read length. Base-calling was perform online during the sequencing procedure with the Real-Time Analysis (RTA) software version 2.4.11 and System Suite Version 2.1.2.1. PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: PLYS PGCGROWTHCONDITIONS
R2 DH10BGFP_pLys_M1_1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: DH10BGFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: M1 PGCGROWTHCONDITIONS
treatment: 15 min after induction with arabinose PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: PSB1C3 PGCGROWTHCONDITIONS
R3 DH10BGFP_pSB1C3_1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: DH10BGFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: None PGCGROWTHCONDITIONS
treatment: 15 min after induction with arabinose PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: PD864 PGCGROWTHCONDITIONS
R6 DH10BGFP_pD864_LacZ_1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: DH10BGFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: LACZ PGCGROWTHCONDITIONS
treatment: 15 min after induction with rhamnose PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: PLYS PGCGROWTHCONDITIONS
R11 DH10BGFP_pLys_1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: DH10BGFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: None PGCGROWTHCONDITIONS
treatment: 60 min after induction with arabinose PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: PLYS PGCGROWTHCONDITIONS
R16 MG1655GFP_pLys_M1_1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: MG1655GFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: M1 PGCGROWTHCONDITIONS
treatment: 15 min after induction with arabinose PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: PSB1C3 PGCGROWTHCONDITIONS
R19 MG1655GFP_Lux_1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: MG1655GFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: Lux PGCGROWTHCONDITIONS
treatment: 15 min after induction with arabinose PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: PSB1C3 PGCGROWTHCONDITIONS
R26 MG1655GFP_Lux_1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: MG1655GFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: Lux PGCGROWTHCONDITIONS
treatment: 60 min after induction with arabinose PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: PD864 PGCGROWTHCONDITIONS
R27 MG1655GFP_pD864_LacZ_1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: MG1655GFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: LACZ PGCGROWTHCONDITIONS
treatment: 60 min after induction with rhamnose PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: None PGCGROWTHCONDITIONS
R29 DH10BGFP_None_1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: DH10BGFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: None PGCGROWTHCONDITIONS
treatment: 15 min PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
B3 DH10BGFP_pSB1C3_2 PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: PSB1C3 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: DH10BGFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: None PGCGROWTHCONDITIONS
treatment: 15 min after induction with arabinose PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
B4 DH10BGFP_pLys_2 PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: PLYS PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: DH10BGFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: None PGCGROWTHCONDITIONS
treatment: 15 min after induction with arabinose PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
B7 DH10BGFP_pD864_2 PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: PD864 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: DH10BGFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: None PGCGROWTHCONDITIONS
treatment: 15 min after induction with rhamnose PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
B9 DH10BGFP_pLys_M1_2 PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: PLYS PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: DH10BGFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: M1 PGCGROWTHCONDITIONS
treatment: 60 min after induction with arabinose PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
B10 DH10BGFP_pSB1C3_2 PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: PSB1C3 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: DH10BGFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: None PGCGROWTHCONDITIONS
treatment: 60 min after induction with arabinose PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
B17 MG1655GFP_pSB1C3_2 PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: PSB1C3 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: MG1655GFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: None PGCGROWTHCONDITIONS
treatment: 15 min after induction with arabinose PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
B22 MG1655GFP_pSB1C3_H3_2 PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: PSB1C3 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: MG1655GFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: H3 PGCGROWTHCONDITIONS
treatment: 60 min after induction with arabinose PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
B26 MG1655GFP_Lux_2 PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: PSB1C3 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: MG1655GFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: Lux PGCGROWTHCONDITIONS
treatment: 60 min after induction with arabinose PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
G5 DH10BGFP_Lux_3 PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: PSB1C3 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: DH10BGFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: Lux PGCGROWTHCONDITIONS
treatment: 15 min after induction with arabinose PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
G6 DH10BGFP_pD864_LacZ_3 PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: PD864 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: DH10BGFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: LACZ PGCGROWTHCONDITIONS
treatment: 15 min after induction with rhamnose PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
G21 MG1655GFP_pD864_3 PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: PD864 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: MG1655GFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: None PGCGROWTHCONDITIONS
treatment: 15 min after induction with rhamnose PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
G23 MG1655GFP_pLys_M1_3 PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: PLYS PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: MG1655GFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: M1 PGCGROWTHCONDITIONS
treatment: 60 min after induction with arabinose PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
G28 MG1655GFP_pD864_3 PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: PD864 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: MG1655GFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: None PGCGROWTHCONDITIONS
treatment: 60 min after induction with rhamnose PGCGROWTHCONDITIONS
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen). PGCGROWTHCONDITIONS
After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
G29 DH10BGFP_None_3 PGCGROWTHCONDITIONS
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit. PGCGROWTHCONDITIONS
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM. PGCGROWTHCONDITIONS
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6 PGCGROWTHCONDITIONS
paired end sequencing with Illumina HiSeq 2500 Sequencer PGCGROWTHCONDITIONS
plasmid: None PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters PGCGROWTHCONDITIONS
strain: DH10BGFP PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene PGCGROWTHCONDITIONS
synthetic circuit: None PGCGROWTHCONDITIONS
treatment: 15 min PGCGROWTHCONDITIONS
3C-seq: 5 µg of a 3C library was suspended in water (final volume 130 µL) and sheared using a Covaris S220 instrument (Duty cycle 5, Intensity 5, cycles/burst 200, time 60 sec for 4 cycles). The DNA was purified and processed according to manufacturer instructions (Paired-End DNA sample Prep Kit – Illumina – PE-930-1001), except that DNA was ligated to custom-made adapters (see Marbouty M. et al, 2015, Mol Cell) for 4 hours at room temperature. Tubes were then incubated at 65°C for 20 minutes. DNA fragments ranging in size from 400 to 900 pb were purified using a PippinPrep apparatus (SAGE Science). For each library, four test PCR reactions were performed to determine the optimal number of PCR cycles (1 or 2 µL of the collected DNA, Illumina primers PE1.0 and PE2.0 using Taq Phusion [Finnzymes]). A large-scale PCR (8 reactions) was then set-up with the number of PCR cycles determined previously. The PCR product was finally purified on Qiagen MinElute columns and subject to paired-end sequenced on an Illumina sequencer. PGCGROWTHCONDITIONS
3C-seq libraries were proccessed using the 3C-seq pipeline available at (https://github.com/koszullab/). PGCGROWTHCONDITIONS
Assignment to restriction fragment PGCGROWTHCONDITIONS
Binning at 5kb. PGCGROWTHCONDITIONS
E coli cells PGCGROWTHCONDITIONS
E. coli cells were grown at 22°C, 30°C and 37°C in either Lennox Broth (LB) or liquid minimal medium A supplemented with 0.12% casamino acids and 0.4% glucose. The cultures were grown to OD600 = 0.2 (early exponential) or 2 (stationary phase). PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Filtering, Mapping quality=30, no ambiguous reads PGCGROWTHCONDITIONS
For 3C-seq: ≈ 1-2 x 109 crosslinked cells (7% formaldehyde, unless otherwise stated ) are suspended in 600 μl Tris 10 mM EDTA 0.5 mM (TE) (pH 8) with 4 μl of lysozyme (35 U/μl; Tebu Bio), and incubated at RT for 20 minutes. SDS is added to the mix (final concentration 0.5%) and the cells are incubated for 10 minutes at RT. 50μl of lysed cells are then transferred in 8 tubes containing 450μL of digestion mix (1X NEB 1 buffer, 1% triton X-100, and 100U HpaII enzyme). DNA is digested for 3 hours at 37°C, split in 4 aliquots, and diluted in 8 ml ligation buffer (1X ligation buffer NEB without ATP, 1 mM ATP, 0.1 mg/ml BSA, 125 Units of T4 DNA ligase 5 U/μl). Ligation is then performed at 16°C for 4 hours, followed by incubation overnight (ON) at 65°C in presence of 250 μg/ml proteinase K and 5 mM EDTA. Precipitation of DNA is performed using an equal volume of 3 M Na-Acetate (pH 5.2) and two volumes of iso-propanol. After one hour at -80°C, DNA is pelleted, suspended in 500μl 1X TE buffer, and incubated for 30 minutes at 37°C in presence of RNAse A (0.03 mg/ml). DNA is then transferred into 2 ml centrifuge tubes, extracted twice with 500 μl phenol-chloroform pH 8.0, precipitated, washed with 1 ml cold ethanol 70% and diluted in 30 μl 1X TE buffer. All tubes are pooled and the resulting 3C library is quantified on gel using Quantity One software (BioRad). PGCGROWTHCONDITIONS
For RNA-seq: total RNA was extracted using RNeasy Protect Bacteria according to manufacturer instructions (QIAGEN - # 74524) PGCGROWTHCONDITIONS
Genome_build: E. coli MG1655 GenBank: U00096.2,total length : 4639675 bp PGCGROWTHCONDITIONS
genotype: F- lambda- ilvG- rfb-50 rph-1 PGCGROWTHCONDITIONS
growth condition: MM + 0.12% casaminoacids +0.4% glucose at 30°C PGCGROWTHCONDITIONS
Iterative alignment, Min-leght=20, step=5, bowtie2 --very-sensitive PGCGROWTHCONDITIONS
Removal of PCR duplicates based on the 20 first bp of the read containing a 6 nt random tag (home made script). PGCGROWTHCONDITIONS
Removal of un-informative events (uncuts, loops etc) as described in Cournac et al. BMC 2012. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-seq of E. coli wt cells in stationary phase 30°C (30h) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: rna-seq: genomic position (middle of the 5kb-bin) to each count. 3C seq: contact maps (2D array of 928 5kb-bins x 928 5kb-bins). PGCGROWTHCONDITIONS
3C-seq: 5 µg of a 3C library was suspended in water (final volume 130 µL) and sheared using a Covaris S220 instrument (Duty cycle 5, Intensity 5, cycles/burst 200, time 60 sec for 4 cycles). The DNA was purified and processed according to manufacturer instructions (Paired-End DNA sample Prep Kit – Illumina – PE-930-1001), except that DNA was ligated to custom-made adapters (see Marbouty M. et al, 2015, Mol Cell) for 4 hours at room temperature. Tubes were then incubated at 65°C for 20 minutes. DNA fragments ranging in size from 400 to 900 pb were purified using a PippinPrep apparatus (SAGE Science). For each library, four test PCR reactions were performed to determine the optimal number of PCR cycles (1 or 2 µL of the collected DNA, Illumina primers PE1.0 and PE2.0 using Taq Phusion [Finnzymes]). A large-scale PCR (8 reactions) was then set-up with the number of PCR cycles determined previously. The PCR product was finally purified on Qiagen MinElute columns and subject to paired-end sequenced on an Illumina sequencer. PGCGROWTHCONDITIONS
3C-seq libraries were proccessed using the 3C-seq pipeline available at (https://github.com/koszullab/). PGCGROWTHCONDITIONS
Assignment to restriction fragment PGCGROWTHCONDITIONS
Binning at 5kb. PGCGROWTHCONDITIONS
E coli cells PGCGROWTHCONDITIONS
E. coli cells were grown at 22°C, 30°C and 37°C in either Lennox Broth (LB) or liquid minimal medium A supplemented with 0.12% casamino acids and 0.4% glucose. The cultures were grown to OD600 = 0.2 (early exponential) or 2 (stationary phase). PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Filtering, Mapping quality=30, no ambiguous reads PGCGROWTHCONDITIONS
For 3C-seq: ≈ 1-2 x 109 crosslinked cells (7% formaldehyde, unless otherwise stated ) are suspended in 600 μl Tris 10 mM EDTA 0.5 mM (TE) (pH 8) with 4 μl of lysozyme (35 U/μl; Tebu Bio), and incubated at RT for 20 minutes. SDS is added to the mix (final concentration 0.5%) and the cells are incubated for 10 minutes at RT. 50μl of lysed cells are then transferred in 8 tubes containing 450μL of digestion mix (1X NEB 1 buffer, 1% triton X-100, and 100U HpaII enzyme). DNA is digested for 3 hours at 37°C, split in 4 aliquots, and diluted in 8 ml ligation buffer (1X ligation buffer NEB without ATP, 1 mM ATP, 0.1 mg/ml BSA, 125 Units of T4 DNA ligase 5 U/μl). Ligation is then performed at 16°C for 4 hours, followed by incubation overnight (ON) at 65°C in presence of 250 μg/ml proteinase K and 5 mM EDTA. Precipitation of DNA is performed using an equal volume of 3 M Na-Acetate (pH 5.2) and two volumes of iso-propanol. After one hour at -80°C, DNA is pelleted, suspended in 500μl 1X TE buffer, and incubated for 30 minutes at 37°C in presence of RNAse A (0.03 mg/ml). DNA is then transferred into 2 ml centrifuge tubes, extracted twice with 500 μl phenol-chloroform pH 8.0, precipitated, washed with 1 ml cold ethanol 70% and diluted in 30 μl 1X TE buffer. All tubes are pooled and the resulting 3C library is quantified on gel using Quantity One software (BioRad). PGCGROWTHCONDITIONS
Genome_build: E. coli MG1655 GenBank: U00096.2,total length : 4639675 bp PGCGROWTHCONDITIONS
genotype: F- lambda- ilvG- rfb-50 rph-1 PGCGROWTHCONDITIONS
growth condition: MM + 0.12% casaminoacids +0.4% glucose at 30°C PGCGROWTHCONDITIONS
Iterative alignment, Min-leght=20, step=5, bowtie2 --very-sensitive PGCGROWTHCONDITIONS
Removal of PCR duplicates based on the 20 first bp of the read containing a 6 nt random tag (home made script). PGCGROWTHCONDITIONS
Removal of un-informative events (uncuts, loops etc) as described in Cournac et al. BMC 2012. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-seq of E. coli wt cells in stationary phase 30°C (30h) -Replicate 1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: rna-seq: genomic position (middle of the 5kb-bin) to each count. 3C seq: contact maps (2D array of 928 5kb-bins x 928 5kb-bins). PGCGROWTHCONDITIONS
Bacterial liquid culture PGCGROWTHCONDITIONS
Counts were depth normalized to a pseudo-reference sample calculated from all samples (ribozero treated samples) or using counts per million counts (total RNA samples). PGCGROWTHCONDITIONS
emptyvec_mRNA_5m_rep1 PGCGROWTHCONDITIONS
ercc spike-in: No PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For each uniquely mapped fragment (ribozero treated samples) or all mapped fragments (total RNA samples), at all aligned positions a count was added. PGCGROWTHCONDITIONS
For ribozero treated samples, counts at all positions were log2 transformed and a cleavage ratio was calculated (+ MazF - empty vector) for assessing MazF cleavage in transcripts. PGCGROWTHCONDITIONS
Genome_build: NCBI reference sequence: NC_000913.2 PGCGROWTHCONDITIONS
Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping. PGCGROWTHCONDITIONS
plasmid: pBAD30-empty PGCGROWTHCONDITIONS
ribozero: Yes PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo). PGCGROWTHCONDITIONS
See publication for complete protocol. Briefly, samples with rRNA subtraction with treated with bacterial Ribo-Zero kit (Illumina). Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were extracted from an acrylamide gel and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols. PGCGROWTHCONDITIONS
Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2. PGCGROWTHCONDITIONS
strain: MG1655 delta_mazF PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: 5m_ribozero_counts_cleavage_ratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for every genomic position at both strands for each ribozero treated sample as well as the average cleavage ratio calculated from all samples. total_RNA_rpm.csv.gz is a list of sequencing depth-normalized counts for every genomic position at both strans for all total RNA samples. PGCGROWTHCONDITIONS
time induction: 5 minutes PGCGROWTHCONDITIONS
Bacterial liquid culture PGCGROWTHCONDITIONS
Counts were depth normalized to a pseudo-reference sample calculated from all samples (ribozero treated samples) or using counts per million counts (total RNA samples). PGCGROWTHCONDITIONS
emptyvec_mRNA_5m_rep2 PGCGROWTHCONDITIONS
ercc spike-in: No PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For each uniquely mapped fragment (ribozero treated samples) or all mapped fragments (total RNA samples), at all aligned positions a count was added. PGCGROWTHCONDITIONS
For ribozero treated samples, counts at all positions were log2 transformed and a cleavage ratio was calculated (+ MazF - empty vector) for assessing MazF cleavage in transcripts. PGCGROWTHCONDITIONS
Genome_build: NCBI reference sequence: NC_000913.2 PGCGROWTHCONDITIONS
Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping. PGCGROWTHCONDITIONS
plasmid: pBAD30-empty PGCGROWTHCONDITIONS
ribozero: Yes PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo). PGCGROWTHCONDITIONS
See publication for complete protocol. Briefly, samples with rRNA subtraction with treated with bacterial Ribo-Zero kit (Illumina). Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were extracted from an acrylamide gel and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols. PGCGROWTHCONDITIONS
Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2. PGCGROWTHCONDITIONS
strain: MG1655 delta_mazF PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: 5m_ribozero_counts_cleavage_ratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for every genomic position at both strands for each ribozero treated sample as well as the average cleavage ratio calculated from all samples. total_RNA_rpm.csv.gz is a list of sequencing depth-normalized counts for every genomic position at both strans for all total RNA samples. PGCGROWTHCONDITIONS
time induction: 5 minutes PGCGROWTHCONDITIONS
Bacterial liquid culture PGCGROWTHCONDITIONS
Counts were depth normalized to a pseudo-reference sample calculated from all samples (ribozero treated samples) or using counts per million counts (total RNA samples). PGCGROWTHCONDITIONS
ercc spike-in: No PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For each uniquely mapped fragment (ribozero treated samples) or all mapped fragments (total RNA samples), at all aligned positions a count was added. PGCGROWTHCONDITIONS
For ribozero treated samples, counts at all positions were log2 transformed and a cleavage ratio was calculated (+ MazF - empty vector) for assessing MazF cleavage in transcripts. PGCGROWTHCONDITIONS
Genome_build: NCBI reference sequence: NC_000913.2 PGCGROWTHCONDITIONS
MazF_mRNA_5m_rep1 PGCGROWTHCONDITIONS
Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping. PGCGROWTHCONDITIONS
plasmid: pBAD30-MazF PGCGROWTHCONDITIONS
ribozero: Yes PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo). PGCGROWTHCONDITIONS
See publication for complete protocol. Briefly, samples with rRNA subtraction with treated with bacterial Ribo-Zero kit (Illumina). Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were extracted from an acrylamide gel and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols. PGCGROWTHCONDITIONS
Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2. PGCGROWTHCONDITIONS
strain: MG1655 delta_mazF PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: 5m_ribozero_counts_cleavage_ratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for every genomic position at both strands for each ribozero treated sample as well as the average cleavage ratio calculated from all samples. total_RNA_rpm.csv.gz is a list of sequencing depth-normalized counts for every genomic position at both strans for all total RNA samples. PGCGROWTHCONDITIONS
time induction: 5 minutes PGCGROWTHCONDITIONS
Bacterial liquid culture PGCGROWTHCONDITIONS
Counts were depth normalized to a pseudo-reference sample calculated from all samples (ribozero treated samples) or using counts per million counts (total RNA samples). PGCGROWTHCONDITIONS
ercc spike-in: No PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For each uniquely mapped fragment (ribozero treated samples) or all mapped fragments (total RNA samples), at all aligned positions a count was added. PGCGROWTHCONDITIONS
For ribozero treated samples, counts at all positions were log2 transformed and a cleavage ratio was calculated (+ MazF - empty vector) for assessing MazF cleavage in transcripts. PGCGROWTHCONDITIONS
Genome_build: NCBI reference sequence: NC_000913.2 PGCGROWTHCONDITIONS
MazF_mRNA_5m_rep2 PGCGROWTHCONDITIONS
Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping. PGCGROWTHCONDITIONS
plasmid: pBAD30-MazF PGCGROWTHCONDITIONS
ribozero: Yes PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo). PGCGROWTHCONDITIONS
See publication for complete protocol. Briefly, samples with rRNA subtraction with treated with bacterial Ribo-Zero kit (Illumina). Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were extracted from an acrylamide gel and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols. PGCGROWTHCONDITIONS
Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2. PGCGROWTHCONDITIONS
strain: MG1655 delta_mazF PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: 5m_ribozero_counts_cleavage_ratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for every genomic position at both strands for each ribozero treated sample as well as the average cleavage ratio calculated from all samples. total_RNA_rpm.csv.gz is a list of sequencing depth-normalized counts for every genomic position at both strans for all total RNA samples. PGCGROWTHCONDITIONS
time induction: 5 minutes PGCGROWTHCONDITIONS
Bacterial liquid culture PGCGROWTHCONDITIONS
Counts were depth normalized to a pseudo-reference sample calculated from all samples (ribozero treated samples) or using counts per million counts (total RNA samples). PGCGROWTHCONDITIONS
emptyvec_totalRNA_5m_rep1 PGCGROWTHCONDITIONS
ercc spike-in: Prior to extraction PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For each uniquely mapped fragment (ribozero treated samples) or all mapped fragments (total RNA samples), at all aligned positions a count was added. PGCGROWTHCONDITIONS
For ribozero treated samples, counts at all positions were log2 transformed and a cleavage ratio was calculated (+ MazF - empty vector) for assessing MazF cleavage in transcripts. PGCGROWTHCONDITIONS
Genome_build: NCBI reference sequence: NC_000913.2 PGCGROWTHCONDITIONS
Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping. PGCGROWTHCONDITIONS
plasmid: pBAD30-empty PGCGROWTHCONDITIONS
ribozero: No PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo). PGCGROWTHCONDITIONS
See publication for complete protocol. Briefly, samples with rRNA subtraction with treated with bacterial Ribo-Zero kit (Illumina). Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were extracted from an acrylamide gel and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols. PGCGROWTHCONDITIONS
Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2. PGCGROWTHCONDITIONS
strain: MG1655 delta_mazF PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: 5m_ribozero_counts_cleavage_ratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for every genomic position at both strands for each ribozero treated sample as well as the average cleavage ratio calculated from all samples. total_RNA_rpm.csv.gz is a list of sequencing depth-normalized counts for every genomic position at both strans for all total RNA samples. PGCGROWTHCONDITIONS
time induction: 5 minutes PGCGROWTHCONDITIONS
Bacterial liquid culture PGCGROWTHCONDITIONS
Counts were depth normalized to a pseudo-reference sample calculated from all samples (ribozero treated samples) or using counts per million counts (total RNA samples). PGCGROWTHCONDITIONS
emptyvec_totalRNA_5m_rep2 PGCGROWTHCONDITIONS
ercc spike-in: Prior to extraction PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For each uniquely mapped fragment (ribozero treated samples) or all mapped fragments (total RNA samples), at all aligned positions a count was added. PGCGROWTHCONDITIONS
For ribozero treated samples, counts at all positions were log2 transformed and a cleavage ratio was calculated (+ MazF - empty vector) for assessing MazF cleavage in transcripts. PGCGROWTHCONDITIONS
Genome_build: NCBI reference sequence: NC_000913.2 PGCGROWTHCONDITIONS
Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping. PGCGROWTHCONDITIONS
plasmid: pBAD30-empty PGCGROWTHCONDITIONS
ribozero: No PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo). PGCGROWTHCONDITIONS
See publication for complete protocol. Briefly, samples with rRNA subtraction with treated with bacterial Ribo-Zero kit (Illumina). Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were extracted from an acrylamide gel and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols. PGCGROWTHCONDITIONS
Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2. PGCGROWTHCONDITIONS
strain: MG1655 delta_mazF PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: 5m_ribozero_counts_cleavage_ratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for every genomic position at both strands for each ribozero treated sample as well as the average cleavage ratio calculated from all samples. total_RNA_rpm.csv.gz is a list of sequencing depth-normalized counts for every genomic position at both strans for all total RNA samples. PGCGROWTHCONDITIONS
time induction: 5 minutes PGCGROWTHCONDITIONS
Bacterial liquid culture PGCGROWTHCONDITIONS
Counts were depth normalized to a pseudo-reference sample calculated from all samples (ribozero treated samples) or using counts per million counts (total RNA samples). PGCGROWTHCONDITIONS
emptyvec_totalRNA_30m_rep1 PGCGROWTHCONDITIONS
ercc spike-in: Prior to extraction PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For each uniquely mapped fragment (ribozero treated samples) or all mapped fragments (total RNA samples), at all aligned positions a count was added. PGCGROWTHCONDITIONS
For ribozero treated samples, counts at all positions were log2 transformed and a cleavage ratio was calculated (+ MazF - empty vector) for assessing MazF cleavage in transcripts. PGCGROWTHCONDITIONS
Genome_build: NCBI reference sequence: NC_000913.2 PGCGROWTHCONDITIONS
Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping. PGCGROWTHCONDITIONS
plasmid: pBAD30-empty PGCGROWTHCONDITIONS
ribozero: No PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo). PGCGROWTHCONDITIONS
See publication for complete protocol. Briefly, samples with rRNA subtraction with treated with bacterial Ribo-Zero kit (Illumina). Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were extracted from an acrylamide gel and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols. PGCGROWTHCONDITIONS
Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2. PGCGROWTHCONDITIONS
strain: MG1655 delta_mazF PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: 5m_ribozero_counts_cleavage_ratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for every genomic position at both strands for each ribozero treated sample as well as the average cleavage ratio calculated from all samples. total_RNA_rpm.csv.gz is a list of sequencing depth-normalized counts for every genomic position at both strans for all total RNA samples. PGCGROWTHCONDITIONS
time induction: 30 minutes PGCGROWTHCONDITIONS
Bacterial liquid culture PGCGROWTHCONDITIONS
Counts were depth normalized to a pseudo-reference sample calculated from all samples (ribozero treated samples) or using counts per million counts (total RNA samples). PGCGROWTHCONDITIONS
emptyvec_totalRNA_30m_rep2 PGCGROWTHCONDITIONS
ercc spike-in: Prior to extraction PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For each uniquely mapped fragment (ribozero treated samples) or all mapped fragments (total RNA samples), at all aligned positions a count was added. PGCGROWTHCONDITIONS
For ribozero treated samples, counts at all positions were log2 transformed and a cleavage ratio was calculated (+ MazF - empty vector) for assessing MazF cleavage in transcripts. PGCGROWTHCONDITIONS
Genome_build: NCBI reference sequence: NC_000913.2 PGCGROWTHCONDITIONS
Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping. PGCGROWTHCONDITIONS
plasmid: pBAD30-empty PGCGROWTHCONDITIONS
ribozero: No PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo). PGCGROWTHCONDITIONS
See publication for complete protocol. Briefly, samples with rRNA subtraction with treated with bacterial Ribo-Zero kit (Illumina). Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were extracted from an acrylamide gel and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols. PGCGROWTHCONDITIONS
Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2. PGCGROWTHCONDITIONS
strain: MG1655 delta_mazF PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: 5m_ribozero_counts_cleavage_ratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for every genomic position at both strands for each ribozero treated sample as well as the average cleavage ratio calculated from all samples. total_RNA_rpm.csv.gz is a list of sequencing depth-normalized counts for every genomic position at both strans for all total RNA samples. PGCGROWTHCONDITIONS
time induction: 30 minutes PGCGROWTHCONDITIONS
Bacterial liquid culture PGCGROWTHCONDITIONS
Counts were depth normalized to a pseudo-reference sample calculated from all samples (ribozero treated samples) or using counts per million counts (total RNA samples). PGCGROWTHCONDITIONS
ercc spike-in: Prior to extraction PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For each uniquely mapped fragment (ribozero treated samples) or all mapped fragments (total RNA samples), at all aligned positions a count was added. PGCGROWTHCONDITIONS
For ribozero treated samples, counts at all positions were log2 transformed and a cleavage ratio was calculated (+ MazF - empty vector) for assessing MazF cleavage in transcripts. PGCGROWTHCONDITIONS
Genome_build: NCBI reference sequence: NC_000913.2 PGCGROWTHCONDITIONS
MazF_totalRNA_5m_rep1 PGCGROWTHCONDITIONS
Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping. PGCGROWTHCONDITIONS
plasmid: pBAD30-MazF PGCGROWTHCONDITIONS
ribozero: No PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo). PGCGROWTHCONDITIONS
See publication for complete protocol. Briefly, samples with rRNA subtraction with treated with bacterial Ribo-Zero kit (Illumina). Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were extracted from an acrylamide gel and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols. PGCGROWTHCONDITIONS
Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2. PGCGROWTHCONDITIONS
strain: MG1655 delta_mazF PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: 5m_ribozero_counts_cleavage_ratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for every genomic position at both strands for each ribozero treated sample as well as the average cleavage ratio calculated from all samples. total_RNA_rpm.csv.gz is a list of sequencing depth-normalized counts for every genomic position at both strans for all total RNA samples. PGCGROWTHCONDITIONS
time induction: 5 minutes PGCGROWTHCONDITIONS
Bacterial liquid culture PGCGROWTHCONDITIONS
Counts were depth normalized to a pseudo-reference sample calculated from all samples (ribozero treated samples) or using counts per million counts (total RNA samples). PGCGROWTHCONDITIONS
ercc spike-in: Prior to extraction PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For each uniquely mapped fragment (ribozero treated samples) or all mapped fragments (total RNA samples), at all aligned positions a count was added. PGCGROWTHCONDITIONS
For ribozero treated samples, counts at all positions were log2 transformed and a cleavage ratio was calculated (+ MazF - empty vector) for assessing MazF cleavage in transcripts. PGCGROWTHCONDITIONS
Genome_build: NCBI reference sequence: NC_000913.2 PGCGROWTHCONDITIONS
MazF_totalRNA_5m_rep2 PGCGROWTHCONDITIONS
Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping. PGCGROWTHCONDITIONS
plasmid: pBAD30-MazF PGCGROWTHCONDITIONS
ribozero: No PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo). PGCGROWTHCONDITIONS
See publication for complete protocol. Briefly, samples with rRNA subtraction with treated with bacterial Ribo-Zero kit (Illumina). Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were extracted from an acrylamide gel and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols. PGCGROWTHCONDITIONS
Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2. PGCGROWTHCONDITIONS
strain: MG1655 delta_mazF PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: 5m_ribozero_counts_cleavage_ratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for every genomic position at both strands for each ribozero treated sample as well as the average cleavage ratio calculated from all samples. total_RNA_rpm.csv.gz is a list of sequencing depth-normalized counts for every genomic position at both strans for all total RNA samples. PGCGROWTHCONDITIONS
time induction: 5 minutes PGCGROWTHCONDITIONS
Bacterial liquid culture PGCGROWTHCONDITIONS
Counts were depth normalized to a pseudo-reference sample calculated from all samples (ribozero treated samples) or using counts per million counts (total RNA samples). PGCGROWTHCONDITIONS
ercc spike-in: Prior to extraction PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For each uniquely mapped fragment (ribozero treated samples) or all mapped fragments (total RNA samples), at all aligned positions a count was added. PGCGROWTHCONDITIONS
For ribozero treated samples, counts at all positions were log2 transformed and a cleavage ratio was calculated (+ MazF - empty vector) for assessing MazF cleavage in transcripts. PGCGROWTHCONDITIONS
Genome_build: NCBI reference sequence: NC_000913.2 PGCGROWTHCONDITIONS
MazF_totalRNA_30m_rep1 PGCGROWTHCONDITIONS
Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping. PGCGROWTHCONDITIONS
plasmid: pBAD30-MazF PGCGROWTHCONDITIONS
ribozero: No PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo). PGCGROWTHCONDITIONS
See publication for complete protocol. Briefly, samples with rRNA subtraction with treated with bacterial Ribo-Zero kit (Illumina). Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were extracted from an acrylamide gel and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols. PGCGROWTHCONDITIONS
Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2. PGCGROWTHCONDITIONS
strain: MG1655 delta_mazF PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: 5m_ribozero_counts_cleavage_ratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for every genomic position at both strands for each ribozero treated sample as well as the average cleavage ratio calculated from all samples. total_RNA_rpm.csv.gz is a list of sequencing depth-normalized counts for every genomic position at both strans for all total RNA samples. PGCGROWTHCONDITIONS
time induction: 30 minutes PGCGROWTHCONDITIONS
Bacterial liquid culture PGCGROWTHCONDITIONS
Counts were depth normalized to a pseudo-reference sample calculated from all samples (ribozero treated samples) or using counts per million counts (total RNA samples). PGCGROWTHCONDITIONS
ercc spike-in: Prior to extraction PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For each uniquely mapped fragment (ribozero treated samples) or all mapped fragments (total RNA samples), at all aligned positions a count was added. PGCGROWTHCONDITIONS
For ribozero treated samples, counts at all positions were log2 transformed and a cleavage ratio was calculated (+ MazF - empty vector) for assessing MazF cleavage in transcripts. PGCGROWTHCONDITIONS
Genome_build: NCBI reference sequence: NC_000913.2 PGCGROWTHCONDITIONS
MazF_totalRNA_30m_rep2 PGCGROWTHCONDITIONS
Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping. PGCGROWTHCONDITIONS
plasmid: pBAD30-MazF PGCGROWTHCONDITIONS
ribozero: No PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo). PGCGROWTHCONDITIONS
See publication for complete protocol. Briefly, samples with rRNA subtraction with treated with bacterial Ribo-Zero kit (Illumina). Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were extracted from an acrylamide gel and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols. PGCGROWTHCONDITIONS
Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2. PGCGROWTHCONDITIONS
strain: MG1655 delta_mazF PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: 5m_ribozero_counts_cleavage_ratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for every genomic position at both strands for each ribozero treated sample as well as the average cleavage ratio calculated from all samples. total_RNA_rpm.csv.gz is a list of sequencing depth-normalized counts for every genomic position at both strans for all total RNA samples. PGCGROWTHCONDITIONS
time induction: 30 minutes PGCGROWTHCONDITIONS
Bacterial liquid culture PGCGROWTHCONDITIONS
Counts were depth normalized to a pseudo-reference sample calculated from all samples (ribozero treated samples) or using counts per million counts (total RNA samples). PGCGROWTHCONDITIONS
ercc spike-in: Prior to extraction PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For each uniquely mapped fragment (ribozero treated samples) or all mapped fragments (total RNA samples), at all aligned positions a count was added. PGCGROWTHCONDITIONS
For ribozero treated samples, counts at all positions were log2 transformed and a cleavage ratio was calculated (+ MazF - empty vector) for assessing MazF cleavage in transcripts. PGCGROWTHCONDITIONS
Genome_build: NCBI reference sequence: NC_000913.2 PGCGROWTHCONDITIONS
MazF_totalRNA_60m_rep1 PGCGROWTHCONDITIONS
Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping. PGCGROWTHCONDITIONS
plasmid: pBAD30-MazF PGCGROWTHCONDITIONS
ribozero: No PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo). PGCGROWTHCONDITIONS
See publication for complete protocol. Briefly, samples with rRNA subtraction with treated with bacterial Ribo-Zero kit (Illumina). Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were extracted from an acrylamide gel and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols. PGCGROWTHCONDITIONS
Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2. PGCGROWTHCONDITIONS
strain: MG1655 delta_mazF PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: 5m_ribozero_counts_cleavage_ratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for every genomic position at both strands for each ribozero treated sample as well as the average cleavage ratio calculated from all samples. total_RNA_rpm.csv.gz is a list of sequencing depth-normalized counts for every genomic position at both strans for all total RNA samples. PGCGROWTHCONDITIONS
time induction: 60 minutes PGCGROWTHCONDITIONS
Bacterial liquid culture PGCGROWTHCONDITIONS
Counts were depth normalized to a pseudo-reference sample calculated from all samples (ribozero treated samples) or using counts per million counts (total RNA samples). PGCGROWTHCONDITIONS
ercc spike-in: Prior to extraction PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For each uniquely mapped fragment (ribozero treated samples) or all mapped fragments (total RNA samples), at all aligned positions a count was added. PGCGROWTHCONDITIONS
For ribozero treated samples, counts at all positions were log2 transformed and a cleavage ratio was calculated (+ MazF - empty vector) for assessing MazF cleavage in transcripts. PGCGROWTHCONDITIONS
Genome_build: NCBI reference sequence: NC_000913.2 PGCGROWTHCONDITIONS
MazF_totalRNA_60m_rep2 PGCGROWTHCONDITIONS
Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping. PGCGROWTHCONDITIONS
plasmid: pBAD30-MazF PGCGROWTHCONDITIONS
ribozero: No PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo). PGCGROWTHCONDITIONS
See publication for complete protocol. Briefly, samples with rRNA subtraction with treated with bacterial Ribo-Zero kit (Illumina). Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were extracted from an acrylamide gel and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols. PGCGROWTHCONDITIONS
Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2. PGCGROWTHCONDITIONS
strain: MG1655 delta_mazF PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: 5m_ribozero_counts_cleavage_ratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for every genomic position at both strands for each ribozero treated sample as well as the average cleavage ratio calculated from all samples. total_RNA_rpm.csv.gz is a list of sequencing depth-normalized counts for every genomic position at both strans for all total RNA samples. PGCGROWTHCONDITIONS
time induction: 60 minutes PGCGROWTHCONDITIONS
Basecalling performed by MiSeq (RTA) PGCGROWTHCONDITIONS
carbon source: Glycerol PGCGROWTHCONDITIONS
cDNA libraries were barcoded with the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA). Libraries were sequenced on the Illumina MiSeq to produce 50 bp single reads. All steps in library construction and sequencing were performed according to manufacturer’s standards. PGCGROWTHCONDITIONS
CF104.3.3_y2 PGCGROWTHCONDITIONS
Compile annotated counts using custom Python script (ExtractMapCounts from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
disease state: cystic fibrosis PGCGROWTHCONDITIONS
E. coli strain isolated from CF patient stool PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS
Filter for map quality >= 20 using Samtools 0.1.18 PGCGROWTHCONDITIONS
Filter out rRNA reads, multi-mapped reads, > 3 mismatches, and gapped mappings using custom Python script (FilterBAM2BAM from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 (U00096.3) PGCGROWTHCONDITIONS
individual: CF patient PGCGROWTHCONDITIONS
Map to MG1655 reference using BWA 0.7.4 (bwa mem, default parameters) PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression level files are tab-delimited text with columns as follows: index, hits, RPKM, RPM, start_position, end_position, strand, feature_type, reference_replicon (type), locus_tag, gene_name, product PGCGROWTHCONDITIONS
Basecalling performed by MiSeq (RTA) PGCGROWTHCONDITIONS
carbon source: Glycerol PGCGROWTHCONDITIONS
cDNA libraries were barcoded with the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA). Libraries were sequenced on the Illumina MiSeq to produce 50 bp single reads. All steps in library construction and sequencing were performed according to manufacturer’s standards. PGCGROWTHCONDITIONS
CF104.3.3_y9 PGCGROWTHCONDITIONS
Compile annotated counts using custom Python script (ExtractMapCounts from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
disease state: cystic fibrosis PGCGROWTHCONDITIONS
E. coli strain isolated from CF patient stool PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS
Filter for map quality >= 20 using Samtools 0.1.18 PGCGROWTHCONDITIONS
Filter out rRNA reads, multi-mapped reads, > 3 mismatches, and gapped mappings using custom Python script (FilterBAM2BAM from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 (U00096.3) PGCGROWTHCONDITIONS
individual: CF patient PGCGROWTHCONDITIONS
Map to MG1655 reference using BWA 0.7.4 (bwa mem, default parameters) PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression level files are tab-delimited text with columns as follows: index, hits, RPKM, RPM, start_position, end_position, strand, feature_type, reference_replicon (type), locus_tag, gene_name, product PGCGROWTHCONDITIONS
Basecalling performed by MiSeq (RTA) PGCGROWTHCONDITIONS
carbon source: Glycerol PGCGROWTHCONDITIONS
cDNA libraries were barcoded with the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA). Libraries were sequenced on the Illumina MiSeq to produce 50 bp single reads. All steps in library construction and sequencing were performed according to manufacturer’s standards. PGCGROWTHCONDITIONS
CF108.4B_y3 PGCGROWTHCONDITIONS
Compile annotated counts using custom Python script (ExtractMapCounts from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
disease state: cystic fibrosis PGCGROWTHCONDITIONS
E. coli strain isolated from CF patient stool PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS
Filter for map quality >= 20 using Samtools 0.1.18 PGCGROWTHCONDITIONS
Filter out rRNA reads, multi-mapped reads, > 3 mismatches, and gapped mappings using custom Python script (FilterBAM2BAM from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 (U00096.3) PGCGROWTHCONDITIONS
individual: CF patient PGCGROWTHCONDITIONS
Map to MG1655 reference using BWA 0.7.4 (bwa mem, default parameters) PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression level files are tab-delimited text with columns as follows: index, hits, RPKM, RPM, start_position, end_position, strand, feature_type, reference_replicon (type), locus_tag, gene_name, product PGCGROWTHCONDITIONS
Basecalling performed by MiSeq (RTA) PGCGROWTHCONDITIONS
carbon source: Glycerol PGCGROWTHCONDITIONS
cDNA libraries were barcoded with the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA). Libraries were sequenced on the Illumina MiSeq to produce 50 bp single reads. All steps in library construction and sequencing were performed according to manufacturer’s standards. PGCGROWTHCONDITIONS
CF108.4B_y8 PGCGROWTHCONDITIONS
Compile annotated counts using custom Python script (ExtractMapCounts from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
disease state: cystic fibrosis PGCGROWTHCONDITIONS
E. coli strain isolated from CF patient stool PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS
Filter for map quality >= 20 using Samtools 0.1.18 PGCGROWTHCONDITIONS
Filter out rRNA reads, multi-mapped reads, > 3 mismatches, and gapped mappings using custom Python script (FilterBAM2BAM from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 (U00096.3) PGCGROWTHCONDITIONS
individual: CF patient PGCGROWTHCONDITIONS
Map to MG1655 reference using BWA 0.7.4 (bwa mem, default parameters) PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression level files are tab-delimited text with columns as follows: index, hits, RPKM, RPM, start_position, end_position, strand, feature_type, reference_replicon (type), locus_tag, gene_name, product PGCGROWTHCONDITIONS
Basecalling performed by MiSeq (RTA) PGCGROWTHCONDITIONS
carbon source: Glycerol PGCGROWTHCONDITIONS
cDNA libraries were barcoded with the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA). Libraries were sequenced on the Illumina MiSeq to produce 50 bp single reads. All steps in library construction and sequencing were performed according to manufacturer’s standards. PGCGROWTHCONDITIONS
Compile annotated counts using custom Python script (ExtractMapCounts from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
CON206.3A_y1 PGCGROWTHCONDITIONS
disease state: control PGCGROWTHCONDITIONS
E. coli strain isolated from healthy child stool PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS
Filter for map quality >= 20 using Samtools 0.1.18 PGCGROWTHCONDITIONS
Filter out rRNA reads, multi-mapped reads, > 3 mismatches, and gapped mappings using custom Python script (FilterBAM2BAM from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 (U00096.3) PGCGROWTHCONDITIONS
individual: healthy child PGCGROWTHCONDITIONS
Map to MG1655 reference using BWA 0.7.4 (bwa mem, default parameters) PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression level files are tab-delimited text with columns as follows: index, hits, RPKM, RPM, start_position, end_position, strand, feature_type, reference_replicon (type), locus_tag, gene_name, product PGCGROWTHCONDITIONS
Basecalling performed by MiSeq (RTA) PGCGROWTHCONDITIONS
carbon source: Glycerol PGCGROWTHCONDITIONS
cDNA libraries were barcoded with the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA). Libraries were sequenced on the Illumina MiSeq to produce 50 bp single reads. All steps in library construction and sequencing were performed according to manufacturer’s standards. PGCGROWTHCONDITIONS
Compile annotated counts using custom Python script (ExtractMapCounts from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
CON206.3A_y2 PGCGROWTHCONDITIONS
disease state: control PGCGROWTHCONDITIONS
E. coli strain isolated from healthy child stool PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS
Filter for map quality >= 20 using Samtools 0.1.18 PGCGROWTHCONDITIONS
Filter out rRNA reads, multi-mapped reads, > 3 mismatches, and gapped mappings using custom Python script (FilterBAM2BAM from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 (U00096.3) PGCGROWTHCONDITIONS
individual: healthy child PGCGROWTHCONDITIONS
Map to MG1655 reference using BWA 0.7.4 (bwa mem, default parameters) PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression level files are tab-delimited text with columns as follows: index, hits, RPKM, RPM, start_position, end_position, strand, feature_type, reference_replicon (type), locus_tag, gene_name, product PGCGROWTHCONDITIONS
Basecalling performed by MiSeq (RTA) PGCGROWTHCONDITIONS
carbon source: Glycerol PGCGROWTHCONDITIONS
cDNA libraries were barcoded with the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA). Libraries were sequenced on the Illumina MiSeq to produce 50 bp single reads. All steps in library construction and sequencing were performed according to manufacturer’s standards. PGCGROWTHCONDITIONS
Compile annotated counts using custom Python script (ExtractMapCounts from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
CON208.3A_y2 PGCGROWTHCONDITIONS
disease state: control PGCGROWTHCONDITIONS
E. coli strain isolated from healthy child stool PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS
Filter for map quality >= 20 using Samtools 0.1.18 PGCGROWTHCONDITIONS
Filter out rRNA reads, multi-mapped reads, > 3 mismatches, and gapped mappings using custom Python script (FilterBAM2BAM from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 (U00096.3) PGCGROWTHCONDITIONS
individual: healthy child PGCGROWTHCONDITIONS
Map to MG1655 reference using BWA 0.7.4 (bwa mem, default parameters) PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression level files are tab-delimited text with columns as follows: index, hits, RPKM, RPM, start_position, end_position, strand, feature_type, reference_replicon (type), locus_tag, gene_name, product PGCGROWTHCONDITIONS
Basecalling performed by MiSeq (RTA) PGCGROWTHCONDITIONS
carbon source: Glycerol PGCGROWTHCONDITIONS
cDNA libraries were barcoded with the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA). Libraries were sequenced on the Illumina MiSeq to produce 50 bp single reads. All steps in library construction and sequencing were performed according to manufacturer’s standards. PGCGROWTHCONDITIONS
Compile annotated counts using custom Python script (ExtractMapCounts from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
CON208.3A_y6 PGCGROWTHCONDITIONS
disease state: control PGCGROWTHCONDITIONS
E. coli strain isolated from healthy child stool PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS
Filter for map quality >= 20 using Samtools 0.1.18 PGCGROWTHCONDITIONS
Filter out rRNA reads, multi-mapped reads, > 3 mismatches, and gapped mappings using custom Python script (FilterBAM2BAM from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 (U00096.3) PGCGROWTHCONDITIONS
individual: healthy child PGCGROWTHCONDITIONS
Map to MG1655 reference using BWA 0.7.4 (bwa mem, default parameters) PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression level files are tab-delimited text with columns as follows: index, hits, RPKM, RPM, start_position, end_position, strand, feature_type, reference_replicon (type), locus_tag, gene_name, product PGCGROWTHCONDITIONS
Basecalling performed by MiSeq (RTA) PGCGROWTHCONDITIONS
carbon source: Glucose PGCGROWTHCONDITIONS
cDNA libraries were barcoded with the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA). Libraries were sequenced on the Illumina MiSeq to produce 50 bp single reads. All steps in library construction and sequencing were performed according to manufacturer’s standards. PGCGROWTHCONDITIONS
CF104.3.3_u1 PGCGROWTHCONDITIONS
Compile annotated counts using custom Python script (ExtractMapCounts from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
disease state: cystic fibrosis PGCGROWTHCONDITIONS
E. coli strain isolated from CF patient stool PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS
Filter for map quality >= 20 using Samtools 0.1.18 PGCGROWTHCONDITIONS
Filter out rRNA reads, multi-mapped reads, > 3 mismatches, and gapped mappings using custom Python script (FilterBAM2BAM from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 (U00096.3) PGCGROWTHCONDITIONS
individual: CF patient PGCGROWTHCONDITIONS
Map to MG1655 reference using BWA 0.7.4 (bwa mem, default parameters) PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression level files are tab-delimited text with columns as follows: index, hits, RPKM, RPM, start_position, end_position, strand, feature_type, reference_replicon (type), locus_tag, gene_name, product PGCGROWTHCONDITIONS
Basecalling performed by MiSeq (RTA) PGCGROWTHCONDITIONS
carbon source: Glucose PGCGROWTHCONDITIONS
cDNA libraries were barcoded with the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA). Libraries were sequenced on the Illumina MiSeq to produce 50 bp single reads. All steps in library construction and sequencing were performed according to manufacturer’s standards. PGCGROWTHCONDITIONS
CF104.3.3_u7 PGCGROWTHCONDITIONS
Compile annotated counts using custom Python script (ExtractMapCounts from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
disease state: cystic fibrosis PGCGROWTHCONDITIONS
E. coli strain isolated from CF patient stool PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS
Filter for map quality >= 20 using Samtools 0.1.18 PGCGROWTHCONDITIONS
Filter out rRNA reads, multi-mapped reads, > 3 mismatches, and gapped mappings using custom Python script (FilterBAM2BAM from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 (U00096.3) PGCGROWTHCONDITIONS
individual: CF patient PGCGROWTHCONDITIONS
Map to MG1655 reference using BWA 0.7.4 (bwa mem, default parameters) PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression level files are tab-delimited text with columns as follows: index, hits, RPKM, RPM, start_position, end_position, strand, feature_type, reference_replicon (type), locus_tag, gene_name, product PGCGROWTHCONDITIONS
Basecalling performed by MiSeq (RTA) PGCGROWTHCONDITIONS
carbon source: Glucose PGCGROWTHCONDITIONS
cDNA libraries were barcoded with the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA). Libraries were sequenced on the Illumina MiSeq to produce 50 bp single reads. All steps in library construction and sequencing were performed according to manufacturer’s standards. PGCGROWTHCONDITIONS
CF108.4B_u1 PGCGROWTHCONDITIONS
Compile annotated counts using custom Python script (ExtractMapCounts from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
disease state: cystic fibrosis PGCGROWTHCONDITIONS
E. coli strain isolated from CF patient stool PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS
Filter for map quality >= 20 using Samtools 0.1.18 PGCGROWTHCONDITIONS
Filter out rRNA reads, multi-mapped reads, > 3 mismatches, and gapped mappings using custom Python script (FilterBAM2BAM from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 (U00096.3) PGCGROWTHCONDITIONS
individual: CF patient PGCGROWTHCONDITIONS
Map to MG1655 reference using BWA 0.7.4 (bwa mem, default parameters) PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression level files are tab-delimited text with columns as follows: index, hits, RPKM, RPM, start_position, end_position, strand, feature_type, reference_replicon (type), locus_tag, gene_name, product PGCGROWTHCONDITIONS
Basecalling performed by MiSeq (RTA) PGCGROWTHCONDITIONS
carbon source: Glucose PGCGROWTHCONDITIONS
cDNA libraries were barcoded with the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA). Libraries were sequenced on the Illumina MiSeq to produce 50 bp single reads. All steps in library construction and sequencing were performed according to manufacturer’s standards. PGCGROWTHCONDITIONS
CF108.4B_u2 PGCGROWTHCONDITIONS
Compile annotated counts using custom Python script (ExtractMapCounts from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
disease state: cystic fibrosis PGCGROWTHCONDITIONS
E. coli strain isolated from CF patient stool PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS
Filter for map quality >= 20 using Samtools 0.1.18 PGCGROWTHCONDITIONS
Filter out rRNA reads, multi-mapped reads, > 3 mismatches, and gapped mappings using custom Python script (FilterBAM2BAM from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 (U00096.3) PGCGROWTHCONDITIONS
individual: CF patient PGCGROWTHCONDITIONS
Map to MG1655 reference using BWA 0.7.4 (bwa mem, default parameters) PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression level files are tab-delimited text with columns as follows: index, hits, RPKM, RPM, start_position, end_position, strand, feature_type, reference_replicon (type), locus_tag, gene_name, product PGCGROWTHCONDITIONS
Basecalling performed by MiSeq (RTA) PGCGROWTHCONDITIONS
carbon source: Glucose PGCGROWTHCONDITIONS
cDNA libraries were barcoded with the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA). Libraries were sequenced on the Illumina MiSeq to produce 50 bp single reads. All steps in library construction and sequencing were performed according to manufacturer’s standards. PGCGROWTHCONDITIONS
Compile annotated counts using custom Python script (ExtractMapCounts from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
CON206.3A_u1 PGCGROWTHCONDITIONS
disease state: control PGCGROWTHCONDITIONS
E. coli strain isolated from healthy child stool PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS
Filter for map quality >= 20 using Samtools 0.1.18 PGCGROWTHCONDITIONS
Filter out rRNA reads, multi-mapped reads, > 3 mismatches, and gapped mappings using custom Python script (FilterBAM2BAM from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 (U00096.3) PGCGROWTHCONDITIONS
individual: healthy child PGCGROWTHCONDITIONS
Map to MG1655 reference using BWA 0.7.4 (bwa mem, default parameters) PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression level files are tab-delimited text with columns as follows: index, hits, RPKM, RPM, start_position, end_position, strand, feature_type, reference_replicon (type), locus_tag, gene_name, product PGCGROWTHCONDITIONS
Basecalling performed by MiSeq (RTA) PGCGROWTHCONDITIONS
carbon source: Glucose PGCGROWTHCONDITIONS
cDNA libraries were barcoded with the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA). Libraries were sequenced on the Illumina MiSeq to produce 50 bp single reads. All steps in library construction and sequencing were performed according to manufacturer’s standards. PGCGROWTHCONDITIONS
Compile annotated counts using custom Python script (ExtractMapCounts from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
CON206.3A_u2 PGCGROWTHCONDITIONS
disease state: control PGCGROWTHCONDITIONS
E. coli strain isolated from healthy child stool PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS
Filter for map quality >= 20 using Samtools 0.1.18 PGCGROWTHCONDITIONS
Filter out rRNA reads, multi-mapped reads, > 3 mismatches, and gapped mappings using custom Python script (FilterBAM2BAM from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 (U00096.3) PGCGROWTHCONDITIONS
individual: healthy child PGCGROWTHCONDITIONS
Map to MG1655 reference using BWA 0.7.4 (bwa mem, default parameters) PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression level files are tab-delimited text with columns as follows: index, hits, RPKM, RPM, start_position, end_position, strand, feature_type, reference_replicon (type), locus_tag, gene_name, product PGCGROWTHCONDITIONS
Basecalling performed by MiSeq (RTA) PGCGROWTHCONDITIONS
carbon source: Glucose PGCGROWTHCONDITIONS
cDNA libraries were barcoded with the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA). Libraries were sequenced on the Illumina MiSeq to produce 50 bp single reads. All steps in library construction and sequencing were performed according to manufacturer’s standards. PGCGROWTHCONDITIONS
Compile annotated counts using custom Python script (ExtractMapCounts from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
CON208.3A_u1 PGCGROWTHCONDITIONS
disease state: control PGCGROWTHCONDITIONS
E. coli strain isolated from healthy child stool PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS
Filter for map quality >= 20 using Samtools 0.1.18 PGCGROWTHCONDITIONS
Filter out rRNA reads, multi-mapped reads, > 3 mismatches, and gapped mappings using custom Python script (FilterBAM2BAM from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 (U00096.3) PGCGROWTHCONDITIONS
individual: healthy child PGCGROWTHCONDITIONS
Map to MG1655 reference using BWA 0.7.4 (bwa mem, default parameters) PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression level files are tab-delimited text with columns as follows: index, hits, RPKM, RPM, start_position, end_position, strand, feature_type, reference_replicon (type), locus_tag, gene_name, product PGCGROWTHCONDITIONS
Basecalling performed by MiSeq (RTA) PGCGROWTHCONDITIONS
carbon source: Glucose PGCGROWTHCONDITIONS
cDNA libraries were barcoded with the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA). Libraries were sequenced on the Illumina MiSeq to produce 50 bp single reads. All steps in library construction and sequencing were performed according to manufacturer’s standards. PGCGROWTHCONDITIONS
Compile annotated counts using custom Python script (ExtractMapCounts from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
CON208.3A_u8 PGCGROWTHCONDITIONS
disease state: control PGCGROWTHCONDITIONS
E. coli strain isolated from healthy child stool PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS
Filter for map quality >= 20 using Samtools 0.1.18 PGCGROWTHCONDITIONS
Filter out rRNA reads, multi-mapped reads, > 3 mismatches, and gapped mappings using custom Python script (FilterBAM2BAM from http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz) PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 (U00096.3) PGCGROWTHCONDITIONS
individual: healthy child PGCGROWTHCONDITIONS
Map to MG1655 reference using BWA 0.7.4 (bwa mem, default parameters) PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression level files are tab-delimited text with columns as follows: index, hits, RPKM, RPM, start_position, end_position, strand, feature_type, reference_replicon (type), locus_tag, gene_name, product PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Functional annotation was done using the Database for Annotation, Visualization and Integrated Discovery (DAVID) Bioinformatics Resources 6.7, NIAID, NIH (http://david.abcc.ncifcrf.gov). PGCGROWTHCONDITIONS
incubation time: 5 hr PGCGROWTHCONDITIONS
Next, a linear model was built for each comparison using the R LIMMA package and statistics for differential expression analysis were computed. To filter for differential expression, two fold or three-fold change with a FDR ≤0.05 were used as the threshold. PGCGROWTHCONDITIONS
PA20 cultures for RNA-seq were grown on T-agar with and without added Sulfamethoxazole-  Trimethoprim at designated levels for the indicated times and temperatures. Working stocks were tested and maintained using LB (Miller formulation) or LB agar. Plasmid pSE380 derivatives were induced by IPTG. PGCGROWTHCONDITIONS
PA20 cultures PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols; rRNAs were removed by Ribozero (gram negative), libraries were prepared using TruSeq protocol. PGCGROWTHCONDITIONS
RNA-seq data were mapped to the E. coli O157:H7 Sakai genome using the Subjunc aligner program from the Subread package (v1.4.6)   (http://bioinf.wehi.edu.au/subread/). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: comma-delimited text files include RPKM values for each Sample PGCGROWTHCONDITIONS
T5_27x_1 PGCGROWTHCONDITIONS
The alignment Bam files were compared against the gene annotation general feature format (GFF) file, and raw counts for each gene were  generated using the featureCounts tool from Subread. The raw counts data of the expressed genes was normalized for RNA composition using the trimmed mean of M values (TMM) method (http://www.ncbi.nlm.nih.gov/pubmed/20196867) from the Empirical analysis of Digital Gene Expression Data in R (EdgeR) package   (https://bioconductor.org/packages/release/bioc/html/edgeR.html), then transformed to log2CPM (counts per million) values using the voom method   (http://www.ncbi.nlm.nih.gov/pubmed/24485249) from the R LIMMA package  (https://bioconductor.org/packages/release/bioc/html/limma.html). PGCGROWTHCONDITIONS
Total RNA samples were isolated using RNAzol RT (Molecular Research Center) by following manufature's instructions. Contaminating DNA was   removed from RNA samples by DNase I digestion using the TURBO DNA-free kit (Ambion). PGCGROWTHCONDITIONS
ug/ml smx / ug/ml tm: 540/108 (27x) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Functional annotation was done using the Database for Annotation, Visualization and Integrated Discovery (DAVID) Bioinformatics Resources 6.7, NIAID, NIH (http://david.abcc.ncifcrf.gov). PGCGROWTHCONDITIONS
incubation time: 5 hr PGCGROWTHCONDITIONS
Next, a linear model was built for each comparison using the R LIMMA package and statistics for differential expression analysis were computed. To filter for differential expression, two fold or three-fold change with a FDR ≤0.05 were used as the threshold. PGCGROWTHCONDITIONS
PA20 cultures for RNA-seq were grown on T-agar with and without added Sulfamethoxazole-  Trimethoprim at designated levels for the indicated times and temperatures. Working stocks were tested and maintained using LB (Miller formulation) or LB agar. Plasmid pSE380 derivatives were induced by IPTG. PGCGROWTHCONDITIONS
PA20 cultures PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols; rRNAs were removed by Ribozero (gram negative), libraries were prepared using TruSeq protocol. PGCGROWTHCONDITIONS
RNA-seq data were mapped to the E. coli O157:H7 Sakai genome using the Subjunc aligner program from the Subread package (v1.4.6)   (http://bioinf.wehi.edu.au/subread/). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: comma-delimited text files include RPKM values for each Sample PGCGROWTHCONDITIONS
T5_1x_4 PGCGROWTHCONDITIONS
The alignment Bam files were compared against the gene annotation general feature format (GFF) file, and raw counts for each gene were  generated using the featureCounts tool from Subread. The raw counts data of the expressed genes was normalized for RNA composition using the trimmed mean of M values (TMM) method (http://www.ncbi.nlm.nih.gov/pubmed/20196867) from the Empirical analysis of Digital Gene Expression Data in R (EdgeR) package   (https://bioconductor.org/packages/release/bioc/html/edgeR.html), then transformed to log2CPM (counts per million) values using the voom method   (http://www.ncbi.nlm.nih.gov/pubmed/24485249) from the R LIMMA package  (https://bioconductor.org/packages/release/bioc/html/limma.html). PGCGROWTHCONDITIONS
Total RNA samples were isolated using RNAzol RT (Molecular Research Center) by following manufature's instructions. Contaminating DNA was   removed from RNA samples by DNase I digestion using the TURBO DNA-free kit (Ambion). PGCGROWTHCONDITIONS
ug/ml smx / ug/ml tm: 20/4 (1x) PGCGROWTHCONDITIONS
1.FHI4.nIND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI4 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000951835 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI4 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
2.FHI4.IND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI4 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000951835 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI4 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
3.FHI6.nIND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI6 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000941895 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI6 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
4.FHI6.IND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI6 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000941895 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI6 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
5.FHI7.nIND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI7 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000936245 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI7 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
6.FHI7.IND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI7 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000936245 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI7 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
7.FHI8.nIND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI8 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000941395 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI8 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
8.FHI8.IND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI8 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000941395 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI8 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
9.FHI9.nIND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI9 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000939195 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
10.FHI9.IND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI9 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000939195 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
11.FHI12.nIND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI12 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000937275 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
12.FHI12.IND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI12 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000937275 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
13.FHI24.nIND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI24 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000936225 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI24 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
15.FHI25.nIND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI25 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000938995 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI25 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
16.FHI25.IND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI25 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000938995 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI25 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
17.FHI27.nIND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI27 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000951875 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI27 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
18.FHI27.IND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI27 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000951875 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI27 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
19.FHI36.nIND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI36 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000753215 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI36 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
20.FHI36.IND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI36 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000753215 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI36 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
21.FHI43.nIND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI43 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000939755 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI43 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
22.FHI43.IND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI43 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000939755 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI43 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
23.FHI48.nIND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI48 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000951915 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI48 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
25.FHI79.nIND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI79 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000939955 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI79 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
26.FHI79.IND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI79 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000939955 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI79 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
27.FHI95.nIND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI95 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000753275 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI95 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
28.FHI95.IND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI95 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000753275 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI95 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
29.St. Olav40.nIND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain St. Olav40 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000965575 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: St. Olav40 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
31.St. Olav104.nIND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain St. Olav104 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000947315 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: St. Olav104 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
32.St. Olav104.IND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain St. Olav104 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000947315 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: St. Olav104 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
33.St. Olav157.nIND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain St. Olav157 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000965635 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: St. Olav157 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
34.St. Olav157.IND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain St. Olav157 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000965635 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: St. Olav157 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
35.St. Olav172.nIND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain St. Olav172 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000752975 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: St. Olav172 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
37.St. Olav174.nIND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain St. Olav174 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000965665 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: St. Olav174 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
38.St. Olav174.IND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain St. Olav174 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000965665 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: St. Olav174 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
39.St. Olav178.nIND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain St. Olav178 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000965555 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: St. Olav178 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
40.St. Olav178.IND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain St. Olav178 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000965555 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: St. Olav178 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
41.St. Olav179.nIND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain St. Olav179 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000965705 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: St. Olav179 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
42.St. Olav179.IND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain St. Olav179 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000965705 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: St. Olav179 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
43.FHI63.nIND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI63 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000946755 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI63 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
44.FHI63.IND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI63 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000946755 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI63 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
45.FHI66.nIND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI66 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000936475 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI66 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
46.FHI66.IND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI66 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000936475 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI66 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
47.FHI83.nIND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI83 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000938695 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI83 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
48.FHI83.IND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain FHI83 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000938695 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: FHI83 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
49.St. Olav17.nIND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain St. Olav17 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000966935 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: St. Olav17 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
50.St. Olav17.IND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain St. Olav17 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000966935 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: St. Olav17 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
51.St. Olav39.IND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain St. Olav39 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000965545 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: St. Olav39 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
52.St. Olav63.nIND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain St. Olav63 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000965625 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: St. Olav63 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
53.St. Olav63.IND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain St. Olav63 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000965625 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: St. Olav63 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
54.St. Olav164 .nIND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain St. Olav164  PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: PVRW00000000 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: St. Olav164  PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
55.St. Olav164 .IND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain St. Olav164  PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: PVRW00000000 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: St. Olav164  PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
56.St. Olav176.IND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain St. Olav176 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000965715 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: St. Olav176 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
57.St. Olav39.nIND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain St. Olav39 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000965545 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: St. Olav39 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
59.St. Olav173.IND.nHUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain St. Olav173 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000965655 PGCGROWTHCONDITIONS
group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
induced/non-induced: Induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: St. Olav173 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
60.St. Olav176.nIND.HUS PGCGROWTHCONDITIONS
A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
E. coli strain St. Olav176 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genome accession: GCA_000965715 PGCGROWTHCONDITIONS
group (hus/non-hus): HUS PGCGROWTHCONDITIONS
induced/non-induced: Non-induced PGCGROWTHCONDITIONS
Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: St. Olav176 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
After chilling on ice, each 100-ml culture was mixed with 25 ml ice-cold ethanol/phenol solution (5% (v/v), water-saturated phenol in 95% (v/v) ethanol).  Cells were harvested by centrifugation at 7,000 g for 2 min at 4 °C, flash-frozen with dry ice, and stored at –80 °C. Two independent cultures for each sample were mixed together for determination of transcriptional profiles. Total RNA was extracted from the collected bacterial cells using TRIzol reagent (Thermo Fisher Scientifc). PGCGROWTHCONDITIONS
Bacterial cultures PGCGROWTHCONDITIONS
culture temperature: 30 °C for 60 min PGCGROWTHCONDITIONS
dnaB-Ts ΔahpC_30°C PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E.coli K12 BW25113 PGCGROWTHCONDITIONS
Illumina Casava1.7 software used for basecalling. PGCGROWTHCONDITIONS
medium: SB broth PGCGROWTHCONDITIONS
Overnight cultures of the dnaB-Ts single mutant (strain 2429) and the dnaB-Ts ΔahpC double mutant (strain 3780) were diluted 100-fold into fresh SB medium (3.2% peptone, 2% yeast extract and 1% NaCl), and they were then grown at 30 °C to early-log phase (OD600 = 0.15).  Next these log-phase cultures were diluted 20-fold into 200 ml pre-warmed, fresh SB medium, and they were grown at 30 °C for another 60 min. PGCGROWTHCONDITIONS
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA was removed from total RNA by using the Ribo-Zero rRNA removal kit. Reverse transcription and cDNA amplification were performed with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech). Libraries were constructed using the Illumina Nextera XT kit and analyzed for concentration , size distribution and quantification of viable sequencing templates via qPCR. PGCGROWTHCONDITIONS
Samples (200-ml) of the above cultures for each strain were split into two aliquots (each 100 ml), and the aliquots were then incubated at 30 °C or 42 °C for another 60 min. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to E.coli K2 BW25113 whole genome using bowtie v0.12.2 PGCGROWTHCONDITIONS
strain: 2429 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. PGCGROWTHCONDITIONS
To generate Illumina-compatible sequencing libraries for each sample, molecular indexes were added to each library, allowing samples to be pooled and sequenced on the Illumina HiSeq 2500 with a 1 x 50 bp single-end configuration. More than 250 million reads were generated per sample, and at least 80% bases had quality scores above Q30. PGCGROWTHCONDITIONS
After chilling on ice, each 100-ml culture was mixed with 25 ml ice-cold ethanol/phenol solution (5% (v/v), water-saturated phenol in 95% (v/v) ethanol).  Cells were harvested by centrifugation at 7,000 g for 2 min at 4 °C, flash-frozen with dry ice, and stored at –80 °C. Two independent cultures for each sample were mixed together for determination of transcriptional profiles. Total RNA was extracted from the collected bacterial cells using TRIzol reagent (Thermo Fisher Scientifc). PGCGROWTHCONDITIONS
Bacterial cultures PGCGROWTHCONDITIONS
culture temperature: 42 °C for 60 min PGCGROWTHCONDITIONS
dnaB-Ts_42°C PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E.coli K12 BW25113 PGCGROWTHCONDITIONS
Illumina Casava1.7 software used for basecalling. PGCGROWTHCONDITIONS
medium: SB broth PGCGROWTHCONDITIONS
Overnight cultures of the dnaB-Ts single mutant (strain 2429) and the dnaB-Ts ΔahpC double mutant (strain 3780) were diluted 100-fold into fresh SB medium (3.2% peptone, 2% yeast extract and 1% NaCl), and they were then grown at 30 °C to early-log phase (OD600 = 0.15).  Next these log-phase cultures were diluted 20-fold into 200 ml pre-warmed, fresh SB medium, and they were grown at 30 °C for another 60 min. PGCGROWTHCONDITIONS
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA was removed from total RNA by using the Ribo-Zero rRNA removal kit. Reverse transcription and cDNA amplification were performed with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech). Libraries were constructed using the Illumina Nextera XT kit and analyzed for concentration , size distribution and quantification of viable sequencing templates via qPCR. PGCGROWTHCONDITIONS
Samples (200-ml) of the above cultures for each strain were split into two aliquots (each 100 ml), and the aliquots were then incubated at 30 °C or 42 °C for another 60 min. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to E.coli K2 BW25113 whole genome using bowtie v0.12.2 PGCGROWTHCONDITIONS
strain: 3780 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. PGCGROWTHCONDITIONS
To generate Illumina-compatible sequencing libraries for each sample, molecular indexes were added to each library, allowing samples to be pooled and sequenced on the Illumina HiSeq 2500 with a 1 x 50 bp single-end configuration. More than 250 million reads were generated per sample, and at least 80% bases had quality scores above Q30. PGCGROWTHCONDITIONS
After chilling on ice, each 100-ml culture was mixed with 25 ml ice-cold ethanol/phenol solution (5% (v/v), water-saturated phenol in 95% (v/v) ethanol).  Cells were harvested by centrifugation at 7,000 g for 2 min at 4 °C, flash-frozen with dry ice, and stored at –80 °C. Two independent cultures for each sample were mixed together for determination of transcriptional profiles. Total RNA was extracted from the collected bacterial cells using TRIzol reagent (Thermo Fisher Scientifc). PGCGROWTHCONDITIONS
Bacterial cultures PGCGROWTHCONDITIONS
culture temperature: 42 °C for 60 min PGCGROWTHCONDITIONS
dnaB-Ts ΔahpC_42°C PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E.coli K12 BW25113 PGCGROWTHCONDITIONS
Illumina Casava1.7 software used for basecalling. PGCGROWTHCONDITIONS
medium: SB broth PGCGROWTHCONDITIONS
Overnight cultures of the dnaB-Ts single mutant (strain 2429) and the dnaB-Ts ΔahpC double mutant (strain 3780) were diluted 100-fold into fresh SB medium (3.2% peptone, 2% yeast extract and 1% NaCl), and they were then grown at 30 °C to early-log phase (OD600 = 0.15).  Next these log-phase cultures were diluted 20-fold into 200 ml pre-warmed, fresh SB medium, and they were grown at 30 °C for another 60 min. PGCGROWTHCONDITIONS
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA was removed from total RNA by using the Ribo-Zero rRNA removal kit. Reverse transcription and cDNA amplification were performed with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech). Libraries were constructed using the Illumina Nextera XT kit and analyzed for concentration , size distribution and quantification of viable sequencing templates via qPCR. PGCGROWTHCONDITIONS
Samples (200-ml) of the above cultures for each strain were split into two aliquots (each 100 ml), and the aliquots were then incubated at 30 °C or 42 °C for another 60 min. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to E.coli K2 BW25113 whole genome using bowtie v0.12.2 PGCGROWTHCONDITIONS
strain: 3780 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. PGCGROWTHCONDITIONS
To generate Illumina-compatible sequencing libraries for each sample, molecular indexes were added to each library, allowing samples to be pooled and sequenced on the Illumina HiSeq 2500 with a 1 x 50 bp single-end configuration. More than 250 million reads were generated per sample, and at least 80% bases had quality scores above Q30. PGCGROWTHCONDITIONS
1 ml aliquot of culture was transferred to pressure vessel and pressurized at 1MPa for 15 min PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
E. coli K-12 MG 1655 was grown  in LB-Miller broth at 37°C ,160rpm to  an O.D.600 nm of 0. 7 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Gene annotation was obtained from the EcoCyc E. coli Database (https://ecocyc.org/). PGCGROWTHCONDITIONS
Genome_build: U00096.3 PGCGROWTHCONDITIONS
HP1 PGCGROWTHCONDITIONS
MiSeq for base calling PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
stimulus: 1 MPa for 15 min PGCGROWTHCONDITIONS
strain: K-12 substr. MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Table of read counts with genes as  rows and samples as columns. PGCGROWTHCONDITIONS
The counts of reads 150 aligning to genomic features were obtained using the 'feaureCounts' function from the R package 'Rsubread' PGCGROWTHCONDITIONS
The lysates were applied to gDNA removal columns and rRNA was removed from total RNA using a Ribo-Zero rRNA removal kit (Illumina, UK) following the manufacture’s instruction for Gram-positive bacteria. The sequencing libraries were prepared from the enriched mRNA using the NEBNext Ultra RNA library prep kit (NEB, UK), and independently indexed using NEBNext multi-plex oligos for Illumina (NEB, UK). The libraries were pooled at equimolar ratios before they were sequenced using MiSeq Reagent Kit v3 600 cycles (Illumina,UK). PGCGROWTHCONDITIONS
The quality of sequencing data was assessed using FastQC, (V11.2) before the reads were trimmed using Trimmomatic (V0.33). PGCGROWTHCONDITIONS
The R package 'DESeq2' (Version 1.12.4) was used to calculate differential gene expression between the LP group and the HP group. PGCGROWTHCONDITIONS
The trimmed reads were aligned against E. 149 coli MG1655 (GenBank: U00096.3) using bowtie2 (Version 2.2.4) PGCGROWTHCONDITIONS
tissue: bacterial cells PGCGROWTHCONDITIONS
Total RNAs from two biological replicate, each with two technical replicates were extracted using the Total RNA Purification Kit (Norgen Biotek, UK) according to the manufacturer’s protocol with the addition of 1 mg/ml lysozyme for cell lysis. PGCGROWTHCONDITIONS
1 ml aliquot of culture was transferred to pressure vessel and pressurized at 1MPa for 15 min PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
E. coli K-12 MG 1655 was grown  in LB-Miller broth at 37°C ,160rpm to  an O.D.600 nm of 0. 7 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Gene annotation was obtained from the EcoCyc E. coli Database (https://ecocyc.org/). PGCGROWTHCONDITIONS
Genome_build: U00096.3 PGCGROWTHCONDITIONS
HP2 PGCGROWTHCONDITIONS
MiSeq for base calling PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
stimulus: 1 MPa for 15 min PGCGROWTHCONDITIONS
strain: K-12 substr. MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Table of read counts with genes as  rows and samples as columns. PGCGROWTHCONDITIONS
The counts of reads 150 aligning to genomic features were obtained using the 'feaureCounts' function from the R package 'Rsubread' PGCGROWTHCONDITIONS
The lysates were applied to gDNA removal columns and rRNA was removed from total RNA using a Ribo-Zero rRNA removal kit (Illumina, UK) following the manufacture’s instruction for Gram-positive bacteria. The sequencing libraries were prepared from the enriched mRNA using the NEBNext Ultra RNA library prep kit (NEB, UK), and independently indexed using NEBNext multi-plex oligos for Illumina (NEB, UK). The libraries were pooled at equimolar ratios before they were sequenced using MiSeq Reagent Kit v3 600 cycles (Illumina,UK). PGCGROWTHCONDITIONS
The quality of sequencing data was assessed using FastQC, (V11.2) before the reads were trimmed using Trimmomatic (V0.33). PGCGROWTHCONDITIONS
The R package 'DESeq2' (Version 1.12.4) was used to calculate differential gene expression between the LP group and the HP group. PGCGROWTHCONDITIONS
The trimmed reads were aligned against E. 149 coli MG1655 (GenBank: U00096.3) using bowtie2 (Version 2.2.4) PGCGROWTHCONDITIONS
tissue: bacterial cells PGCGROWTHCONDITIONS
Total RNAs from two biological replicate, each with two technical replicates were extracted using the Total RNA Purification Kit (Norgen Biotek, UK) according to the manufacturer’s protocol with the addition of 1 mg/ml lysozyme for cell lysis. PGCGROWTHCONDITIONS
1 ml aliquot of culture was transferred to pressure vessel and pressurized at 1MPa for 15 min PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
E. coli K-12 MG 1655 was grown  in LB-Miller broth at 37°C ,160rpm to  an O.D.600 nm of 0. 7 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Gene annotation was obtained from the EcoCyc E. coli Database (https://ecocyc.org/). PGCGROWTHCONDITIONS
Genome_build: U00096.3 PGCGROWTHCONDITIONS
HP3 PGCGROWTHCONDITIONS
MiSeq for base calling PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
stimulus: 1 MPa for 15 min PGCGROWTHCONDITIONS
strain: K-12 substr. MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Table of read counts with genes as  rows and samples as columns. PGCGROWTHCONDITIONS
The counts of reads 150 aligning to genomic features were obtained using the 'feaureCounts' function from the R package 'Rsubread' PGCGROWTHCONDITIONS
The lysates were applied to gDNA removal columns and rRNA was removed from total RNA using a Ribo-Zero rRNA removal kit (Illumina, UK) following the manufacture’s instruction for Gram-positive bacteria. The sequencing libraries were prepared from the enriched mRNA using the NEBNext Ultra RNA library prep kit (NEB, UK), and independently indexed using NEBNext multi-plex oligos for Illumina (NEB, UK). The libraries were pooled at equimolar ratios before they were sequenced using MiSeq Reagent Kit v3 600 cycles (Illumina,UK). PGCGROWTHCONDITIONS
The quality of sequencing data was assessed using FastQC, (V11.2) before the reads were trimmed using Trimmomatic (V0.33). PGCGROWTHCONDITIONS
The R package 'DESeq2' (Version 1.12.4) was used to calculate differential gene expression between the LP group and the HP group. PGCGROWTHCONDITIONS
The trimmed reads were aligned against E. 149 coli MG1655 (GenBank: U00096.3) using bowtie2 (Version 2.2.4) PGCGROWTHCONDITIONS
tissue: bacterial cells PGCGROWTHCONDITIONS
Total RNAs from two biological replicate, each with two technical replicates were extracted using the Total RNA Purification Kit (Norgen Biotek, UK) according to the manufacturer’s protocol with the addition of 1 mg/ml lysozyme for cell lysis. PGCGROWTHCONDITIONS
1 ml aliquot of culture was transferred to pressure vessel and pressurized at 1MPa for 15 min PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
E. coli K-12 MG 1655 was grown  in LB-Miller broth at 37°C ,160rpm to  an O.D.600 nm of 0. 7 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Gene annotation was obtained from the EcoCyc E. coli Database (https://ecocyc.org/). PGCGROWTHCONDITIONS
Genome_build: U00096.3 PGCGROWTHCONDITIONS
HP4 PGCGROWTHCONDITIONS
MiSeq for base calling PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
stimulus: 1 MPa for 15 min PGCGROWTHCONDITIONS
strain: K-12 substr. MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Table of read counts with genes as  rows and samples as columns. PGCGROWTHCONDITIONS
The counts of reads 150 aligning to genomic features were obtained using the 'feaureCounts' function from the R package 'Rsubread' PGCGROWTHCONDITIONS
The lysates were applied to gDNA removal columns and rRNA was removed from total RNA using a Ribo-Zero rRNA removal kit (Illumina, UK) following the manufacture’s instruction for Gram-positive bacteria. The sequencing libraries were prepared from the enriched mRNA using the NEBNext Ultra RNA library prep kit (NEB, UK), and independently indexed using NEBNext multi-plex oligos for Illumina (NEB, UK). The libraries were pooled at equimolar ratios before they were sequenced using MiSeq Reagent Kit v3 600 cycles (Illumina,UK). PGCGROWTHCONDITIONS
The quality of sequencing data was assessed using FastQC, (V11.2) before the reads were trimmed using Trimmomatic (V0.33). PGCGROWTHCONDITIONS
The R package 'DESeq2' (Version 1.12.4) was used to calculate differential gene expression between the LP group and the HP group. PGCGROWTHCONDITIONS
The trimmed reads were aligned against E. 149 coli MG1655 (GenBank: U00096.3) using bowtie2 (Version 2.2.4) PGCGROWTHCONDITIONS
tissue: bacterial cells PGCGROWTHCONDITIONS
Total RNAs from two biological replicate, each with two technical replicates were extracted using the Total RNA Purification Kit (Norgen Biotek, UK) according to the manufacturer’s protocol with the addition of 1 mg/ml lysozyme for cell lysis. PGCGROWTHCONDITIONS
1 ml aliquot of culture was transferred to pressure vessel and pressurized at 1MPa for 15 min PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
E. coli K-12 MG 1655 was grown  in LB-Miller broth at 37°C ,160rpm to  an O.D.600 nm of 0. 7 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Gene annotation was obtained from the EcoCyc E. coli Database (https://ecocyc.org/). PGCGROWTHCONDITIONS
Genome_build: U00096.3 PGCGROWTHCONDITIONS
LP1 PGCGROWTHCONDITIONS
MiSeq for base calling PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
stimulus: Control PGCGROWTHCONDITIONS
strain: K-12 substr. MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Table of read counts with genes as  rows and samples as columns. PGCGROWTHCONDITIONS
The counts of reads 150 aligning to genomic features were obtained using the 'feaureCounts' function from the R package 'Rsubread' PGCGROWTHCONDITIONS
The lysates were applied to gDNA removal columns and rRNA was removed from total RNA using a Ribo-Zero rRNA removal kit (Illumina, UK) following the manufacture’s instruction for Gram-positive bacteria. The sequencing libraries were prepared from the enriched mRNA using the NEBNext Ultra RNA library prep kit (NEB, UK), and independently indexed using NEBNext multi-plex oligos for Illumina (NEB, UK). The libraries were pooled at equimolar ratios before they were sequenced using MiSeq Reagent Kit v3 600 cycles (Illumina,UK). PGCGROWTHCONDITIONS
The quality of sequencing data was assessed using FastQC, (V11.2) before the reads were trimmed using Trimmomatic (V0.33). PGCGROWTHCONDITIONS
The R package 'DESeq2' (Version 1.12.4) was used to calculate differential gene expression between the LP group and the HP group. PGCGROWTHCONDITIONS
The trimmed reads were aligned against E. 149 coli MG1655 (GenBank: U00096.3) using bowtie2 (Version 2.2.4) PGCGROWTHCONDITIONS
tissue: bacterial cells PGCGROWTHCONDITIONS
Total RNAs from two biological replicate, each with two technical replicates were extracted using the Total RNA Purification Kit (Norgen Biotek, UK) according to the manufacturer’s protocol with the addition of 1 mg/ml lysozyme for cell lysis. PGCGROWTHCONDITIONS
1 ml aliquot of culture was transferred to pressure vessel and pressurized at 1MPa for 15 min PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
E. coli K-12 MG 1655 was grown  in LB-Miller broth at 37°C ,160rpm to  an O.D.600 nm of 0. 7 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Gene annotation was obtained from the EcoCyc E. coli Database (https://ecocyc.org/). PGCGROWTHCONDITIONS
Genome_build: U00096.3 PGCGROWTHCONDITIONS
LP2 PGCGROWTHCONDITIONS
MiSeq for base calling PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
stimulus: Control PGCGROWTHCONDITIONS
strain: K-12 substr. MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Table of read counts with genes as  rows and samples as columns. PGCGROWTHCONDITIONS
The counts of reads 150 aligning to genomic features were obtained using the 'feaureCounts' function from the R package 'Rsubread' PGCGROWTHCONDITIONS
The lysates were applied to gDNA removal columns and rRNA was removed from total RNA using a Ribo-Zero rRNA removal kit (Illumina, UK) following the manufacture’s instruction for Gram-positive bacteria. The sequencing libraries were prepared from the enriched mRNA using the NEBNext Ultra RNA library prep kit (NEB, UK), and independently indexed using NEBNext multi-plex oligos for Illumina (NEB, UK). The libraries were pooled at equimolar ratios before they were sequenced using MiSeq Reagent Kit v3 600 cycles (Illumina,UK). PGCGROWTHCONDITIONS
The quality of sequencing data was assessed using FastQC, (V11.2) before the reads were trimmed using Trimmomatic (V0.33). PGCGROWTHCONDITIONS
The R package 'DESeq2' (Version 1.12.4) was used to calculate differential gene expression between the LP group and the HP group. PGCGROWTHCONDITIONS
The trimmed reads were aligned against E. 149 coli MG1655 (GenBank: U00096.3) using bowtie2 (Version 2.2.4) PGCGROWTHCONDITIONS
tissue: bacterial cells PGCGROWTHCONDITIONS
Total RNAs from two biological replicate, each with two technical replicates were extracted using the Total RNA Purification Kit (Norgen Biotek, UK) according to the manufacturer’s protocol with the addition of 1 mg/ml lysozyme for cell lysis. PGCGROWTHCONDITIONS
1 ml aliquot of culture was transferred to pressure vessel and pressurized at 1MPa for 15 min PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
E. coli K-12 MG 1655 was grown  in LB-Miller broth at 37°C ,160rpm to  an O.D.600 nm of 0. 7 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Gene annotation was obtained from the EcoCyc E. coli Database (https://ecocyc.org/). PGCGROWTHCONDITIONS
Genome_build: U00096.3 PGCGROWTHCONDITIONS
LP3 PGCGROWTHCONDITIONS
MiSeq for base calling PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
stimulus: Control PGCGROWTHCONDITIONS
strain: K-12 substr. MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Table of read counts with genes as  rows and samples as columns. PGCGROWTHCONDITIONS
The counts of reads 150 aligning to genomic features were obtained using the 'feaureCounts' function from the R package 'Rsubread' PGCGROWTHCONDITIONS
The lysates were applied to gDNA removal columns and rRNA was removed from total RNA using a Ribo-Zero rRNA removal kit (Illumina, UK) following the manufacture’s instruction for Gram-positive bacteria. The sequencing libraries were prepared from the enriched mRNA using the NEBNext Ultra RNA library prep kit (NEB, UK), and independently indexed using NEBNext multi-plex oligos for Illumina (NEB, UK). The libraries were pooled at equimolar ratios before they were sequenced using MiSeq Reagent Kit v3 600 cycles (Illumina,UK). PGCGROWTHCONDITIONS
The quality of sequencing data was assessed using FastQC, (V11.2) before the reads were trimmed using Trimmomatic (V0.33). PGCGROWTHCONDITIONS
The R package 'DESeq2' (Version 1.12.4) was used to calculate differential gene expression between the LP group and the HP group. PGCGROWTHCONDITIONS
The trimmed reads were aligned against E. 149 coli MG1655 (GenBank: U00096.3) using bowtie2 (Version 2.2.4) PGCGROWTHCONDITIONS
tissue: bacterial cells PGCGROWTHCONDITIONS
Total RNAs from two biological replicate, each with two technical replicates were extracted using the Total RNA Purification Kit (Norgen Biotek, UK) according to the manufacturer’s protocol with the addition of 1 mg/ml lysozyme for cell lysis. PGCGROWTHCONDITIONS
1 ml aliquot of culture was transferred to pressure vessel and pressurized at 1MPa for 15 min PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
E. coli K-12 MG 1655 was grown  in LB-Miller broth at 37°C ,160rpm to  an O.D.600 nm of 0. 7 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Gene annotation was obtained from the EcoCyc E. coli Database (https://ecocyc.org/). PGCGROWTHCONDITIONS
Genome_build: U00096.3 PGCGROWTHCONDITIONS
LP4 PGCGROWTHCONDITIONS
MiSeq for base calling PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
stimulus: Control PGCGROWTHCONDITIONS
strain: K-12 substr. MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Table of read counts with genes as  rows and samples as columns. PGCGROWTHCONDITIONS
The counts of reads 150 aligning to genomic features were obtained using the 'feaureCounts' function from the R package 'Rsubread' PGCGROWTHCONDITIONS
The lysates were applied to gDNA removal columns and rRNA was removed from total RNA using a Ribo-Zero rRNA removal kit (Illumina, UK) following the manufacture’s instruction for Gram-positive bacteria. The sequencing libraries were prepared from the enriched mRNA using the NEBNext Ultra RNA library prep kit (NEB, UK), and independently indexed using NEBNext multi-plex oligos for Illumina (NEB, UK). The libraries were pooled at equimolar ratios before they were sequenced using MiSeq Reagent Kit v3 600 cycles (Illumina,UK). PGCGROWTHCONDITIONS
The quality of sequencing data was assessed using FastQC, (V11.2) before the reads were trimmed using Trimmomatic (V0.33). PGCGROWTHCONDITIONS
The R package 'DESeq2' (Version 1.12.4) was used to calculate differential gene expression between the LP group and the HP group. PGCGROWTHCONDITIONS
The trimmed reads were aligned against E. 149 coli MG1655 (GenBank: U00096.3) using bowtie2 (Version 2.2.4) PGCGROWTHCONDITIONS
tissue: bacterial cells PGCGROWTHCONDITIONS
Total RNAs from two biological replicate, each with two technical replicates were extracted using the Total RNA Purification Kit (Norgen Biotek, UK) according to the manufacturer’s protocol with the addition of 1 mg/ml lysozyme for cell lysis. PGCGROWTHCONDITIONS
After exposed under the red light with a specific ON/OFF frequency for 10 hours, 1ml bacterial culture was sampled and the bacterial cells were collected at 4 °C. The total RNA of E. coli was extracted using RNAprep pure Cell/Bacteria Kit (TIANGEN, DP430) and preserved at -80 °C. PGCGROWTHCONDITIONS
BW25113 PGCGROWTHCONDITIONS
envz600 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
input signal frequency: 1/600 Hz PGCGROWTHCONDITIONS
In the 15 ml centrifuge tube (Corning, 430791), the overnight culture was diluted to 2ml in fresh LB medium containing Ampicillin (50 ng/μl), Chloramphenicol (170 ng/μl) and IPTG (0.5mM) to reach OD600 = 0.01. The LED tube was screwed into the centrifuge tube and connected with the control box. Then the power of the control box was turned on and the LED frequency input was generated. At last, the 15 ml centrifuge tube with LED tube was put into the Thermomixer comfort (Eppendorf) and shaken at 650 rpm and 37°C for 10 hours. PGCGROWTHCONDITIONS
PCA analysis was performed using the top 500 genes with the most variations. PGCGROWTHCONDITIONS
Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) at 37°C overnight. A single colony was diluted in 2.5ml LB medium containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) and was shaken at 250 rpm and 37°C overnight. PGCGROWTHCONDITIONS
plasmid: pLCenvZ, pPCB (wild type) PGCGROWTHCONDITIONS
Read counts per gene determined using HTseq count before normalized using DESeq2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were mapped to the E. coli genome with bowtie2 PGCGROWTHCONDITIONS
strain: JW3367 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The txt file includes the gene expression profiles of all the samples. The xlsx file contains the PC1 and PC2 values of all the samples. PGCGROWTHCONDITIONS
After exposed under the red light with a specific ON/OFF frequency for 10 hours, 1ml bacterial culture was sampled and the bacterial cells were collected at 4 °C. The total RNA of E. coli was extracted using RNAprep pure Cell/Bacteria Kit (TIANGEN, DP430) and preserved at -80 °C. PGCGROWTHCONDITIONS
BW25113 PGCGROWTHCONDITIONS
envz900 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
input signal frequency: 1/900 Hz PGCGROWTHCONDITIONS
In the 15 ml centrifuge tube (Corning, 430791), the overnight culture was diluted to 2ml in fresh LB medium containing Ampicillin (50 ng/μl), Chloramphenicol (170 ng/μl) and IPTG (0.5mM) to reach OD600 = 0.01. The LED tube was screwed into the centrifuge tube and connected with the control box. Then the power of the control box was turned on and the LED frequency input was generated. At last, the 15 ml centrifuge tube with LED tube was put into the Thermomixer comfort (Eppendorf) and shaken at 650 rpm and 37°C for 10 hours. PGCGROWTHCONDITIONS
PCA analysis was performed using the top 500 genes with the most variations. PGCGROWTHCONDITIONS
Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) at 37°C overnight. A single colony was diluted in 2.5ml LB medium containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) and was shaken at 250 rpm and 37°C overnight. PGCGROWTHCONDITIONS
plasmid: pLCenvZ, pPCB (wild type) PGCGROWTHCONDITIONS
Read counts per gene determined using HTseq count before normalized using DESeq2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were mapped to the E. coli genome with bowtie2 PGCGROWTHCONDITIONS
strain: JW3367 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The txt file includes the gene expression profiles of all the samples. The xlsx file contains the PC1 and PC2 values of all the samples. PGCGROWTHCONDITIONS
After exposed under the red light with a specific ON/OFF frequency for 10 hours, 1ml bacterial culture was sampled and the bacterial cells were collected at 4 °C. The total RNA of E. coli was extracted using RNAprep pure Cell/Bacteria Kit (TIANGEN, DP430) and preserved at -80 °C. PGCGROWTHCONDITIONS
BW25113 PGCGROWTHCONDITIONS
envz3600 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
input signal frequency: 1/3600 Hz PGCGROWTHCONDITIONS
In the 15 ml centrifuge tube (Corning, 430791), the overnight culture was diluted to 2ml in fresh LB medium containing Ampicillin (50 ng/μl), Chloramphenicol (170 ng/μl) and IPTG (0.5mM) to reach OD600 = 0.01. The LED tube was screwed into the centrifuge tube and connected with the control box. Then the power of the control box was turned on and the LED frequency input was generated. At last, the 15 ml centrifuge tube with LED tube was put into the Thermomixer comfort (Eppendorf) and shaken at 650 rpm and 37°C for 10 hours. PGCGROWTHCONDITIONS
PCA analysis was performed using the top 500 genes with the most variations. PGCGROWTHCONDITIONS
Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) at 37°C overnight. A single colony was diluted in 2.5ml LB medium containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) and was shaken at 250 rpm and 37°C overnight. PGCGROWTHCONDITIONS
plasmid: pLCenvZ, pPCB (wild type) PGCGROWTHCONDITIONS
Read counts per gene determined using HTseq count before normalized using DESeq2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were mapped to the E. coli genome with bowtie2 PGCGROWTHCONDITIONS
strain: JW3367 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The txt file includes the gene expression profiles of all the samples. The xlsx file contains the PC1 and PC2 values of all the samples. PGCGROWTHCONDITIONS
After exposed under the red light with a specific ON/OFF frequency for 10 hours, 1ml bacterial culture was sampled and the bacterial cells were collected at 4 °C. The total RNA of E. coli was extracted using RNAprep pure Cell/Bacteria Kit (TIANGEN, DP430) and preserved at -80 °C. PGCGROWTHCONDITIONS
BW25113 PGCGROWTHCONDITIONS
envzM600 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
input signal frequency: 1/600 Hz PGCGROWTHCONDITIONS
In the 15 ml centrifuge tube (Corning, 430791), the overnight culture was diluted to 2ml in fresh LB medium containing Ampicillin (50 ng/μl), Chloramphenicol (170 ng/μl) and IPTG (0.5mM) to reach OD600 = 0.01. The LED tube was screwed into the centrifuge tube and connected with the control box. Then the power of the control box was turned on and the LED frequency input was generated. At last, the 15 ml centrifuge tube with LED tube was put into the Thermomixer comfort (Eppendorf) and shaken at 650 rpm and 37°C for 10 hours. PGCGROWTHCONDITIONS
PCA analysis was performed using the top 500 genes with the most variations. PGCGROWTHCONDITIONS
plasmid: pLCenvZM, pPCB (mutation) PGCGROWTHCONDITIONS
Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) at 37°C overnight. A single colony was diluted in 2.5ml LB medium containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) and was shaken at 250 rpm and 37°C overnight. PGCGROWTHCONDITIONS
Read counts per gene determined using HTseq count before normalized using DESeq2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were mapped to the E. coli genome with bowtie2 PGCGROWTHCONDITIONS
strain: JW3367 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The txt file includes the gene expression profiles of all the samples. The xlsx file contains the PC1 and PC2 values of all the samples. PGCGROWTHCONDITIONS
After exposed under the red light with a specific ON/OFF frequency for 10 hours, 1ml bacterial culture was sampled and the bacterial cells were collected at 4 °C. The total RNA of E. coli was extracted using RNAprep pure Cell/Bacteria Kit (TIANGEN, DP430) and preserved at -80 °C. PGCGROWTHCONDITIONS
BW25113 PGCGROWTHCONDITIONS
envzM900 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
input signal frequency: 1/900 Hz PGCGROWTHCONDITIONS
In the 15 ml centrifuge tube (Corning, 430791), the overnight culture was diluted to 2ml in fresh LB medium containing Ampicillin (50 ng/μl), Chloramphenicol (170 ng/μl) and IPTG (0.5mM) to reach OD600 = 0.01. The LED tube was screwed into the centrifuge tube and connected with the control box. Then the power of the control box was turned on and the LED frequency input was generated. At last, the 15 ml centrifuge tube with LED tube was put into the Thermomixer comfort (Eppendorf) and shaken at 650 rpm and 37°C for 10 hours. PGCGROWTHCONDITIONS
PCA analysis was performed using the top 500 genes with the most variations. PGCGROWTHCONDITIONS
plasmid: pLCenvZM, pPCB (mutation) PGCGROWTHCONDITIONS
Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) at 37°C overnight. A single colony was diluted in 2.5ml LB medium containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) and was shaken at 250 rpm and 37°C overnight. PGCGROWTHCONDITIONS
Read counts per gene determined using HTseq count before normalized using DESeq2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were mapped to the E. coli genome with bowtie2 PGCGROWTHCONDITIONS
strain: JW3367 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The txt file includes the gene expression profiles of all the samples. The xlsx file contains the PC1 and PC2 values of all the samples. PGCGROWTHCONDITIONS
After exposed under the red light with a specific ON/OFF frequency for 10 hours, 1ml bacterial culture was sampled and the bacterial cells were collected at 4 °C. The total RNA of E. coli was extracted using RNAprep pure Cell/Bacteria Kit (TIANGEN, DP430) and preserved at -80 °C. PGCGROWTHCONDITIONS
BW25113 PGCGROWTHCONDITIONS
envzM1200 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
input signal frequency: 1/1200 Hz PGCGROWTHCONDITIONS
In the 15 ml centrifuge tube (Corning, 430791), the overnight culture was diluted to 2ml in fresh LB medium containing Ampicillin (50 ng/μl), Chloramphenicol (170 ng/μl) and IPTG (0.5mM) to reach OD600 = 0.01. The LED tube was screwed into the centrifuge tube and connected with the control box. Then the power of the control box was turned on and the LED frequency input was generated. At last, the 15 ml centrifuge tube with LED tube was put into the Thermomixer comfort (Eppendorf) and shaken at 650 rpm and 37°C for 10 hours. PGCGROWTHCONDITIONS
PCA analysis was performed using the top 500 genes with the most variations. PGCGROWTHCONDITIONS
plasmid: pLCenvZM, pPCB (mutation) PGCGROWTHCONDITIONS
Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) at 37°C overnight. A single colony was diluted in 2.5ml LB medium containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) and was shaken at 250 rpm and 37°C overnight. PGCGROWTHCONDITIONS
Read counts per gene determined using HTseq count before normalized using DESeq2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were mapped to the E. coli genome with bowtie2 PGCGROWTHCONDITIONS
strain: JW3367 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The txt file includes the gene expression profiles of all the samples. The xlsx file contains the PC1 and PC2 values of all the samples. PGCGROWTHCONDITIONS
After exposed under the red light with a specific ON/OFF frequency for 10 hours, 1ml bacterial culture was sampled and the bacterial cells were collected at 4 °C. The total RNA of E. coli was extracted using RNAprep pure Cell/Bacteria Kit (TIANGEN, DP430) and preserved at -80 °C. PGCGROWTHCONDITIONS
BW25113 PGCGROWTHCONDITIONS
envzM2400 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
input signal frequency: 1/2400 Hz PGCGROWTHCONDITIONS
In the 15 ml centrifuge tube (Corning, 430791), the overnight culture was diluted to 2ml in fresh LB medium containing Ampicillin (50 ng/μl), Chloramphenicol (170 ng/μl) and IPTG (0.5mM) to reach OD600 = 0.01. The LED tube was screwed into the centrifuge tube and connected with the control box. Then the power of the control box was turned on and the LED frequency input was generated. At last, the 15 ml centrifuge tube with LED tube was put into the Thermomixer comfort (Eppendorf) and shaken at 650 rpm and 37°C for 10 hours. PGCGROWTHCONDITIONS
PCA analysis was performed using the top 500 genes with the most variations. PGCGROWTHCONDITIONS
plasmid: pLCenvZM, pPCB (mutation) PGCGROWTHCONDITIONS
Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) at 37°C overnight. A single colony was diluted in 2.5ml LB medium containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) and was shaken at 250 rpm and 37°C overnight. PGCGROWTHCONDITIONS
Read counts per gene determined using HTseq count before normalized using DESeq2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were mapped to the E. coli genome with bowtie2 PGCGROWTHCONDITIONS
strain: JW3367 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The txt file includes the gene expression profiles of all the samples. The xlsx file contains the PC1 and PC2 values of all the samples. PGCGROWTHCONDITIONS
After exposed under the red light with a specific ON/OFF frequency for 10 hours, 1ml bacterial culture was sampled and the bacterial cells were collected at 4 °C. The total RNA of E. coli was extracted using RNAprep pure Cell/Bacteria Kit (TIANGEN, DP430) and preserved at -80 °C. PGCGROWTHCONDITIONS
BW25113 PGCGROWTHCONDITIONS
envzM3600 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
input signal frequency: 1/3600 Hz PGCGROWTHCONDITIONS
In the 15 ml centrifuge tube (Corning, 430791), the overnight culture was diluted to 2ml in fresh LB medium containing Ampicillin (50 ng/μl), Chloramphenicol (170 ng/μl) and IPTG (0.5mM) to reach OD600 = 0.01. The LED tube was screwed into the centrifuge tube and connected with the control box. Then the power of the control box was turned on and the LED frequency input was generated. At last, the 15 ml centrifuge tube with LED tube was put into the Thermomixer comfort (Eppendorf) and shaken at 650 rpm and 37°C for 10 hours. PGCGROWTHCONDITIONS
PCA analysis was performed using the top 500 genes with the most variations. PGCGROWTHCONDITIONS
plasmid: pLCenvZM, pPCB (mutation) PGCGROWTHCONDITIONS
Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) at 37°C overnight. A single colony was diluted in 2.5ml LB medium containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) and was shaken at 250 rpm and 37°C overnight. PGCGROWTHCONDITIONS
Read counts per gene determined using HTseq count before normalized using DESeq2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were mapped to the E. coli genome with bowtie2 PGCGROWTHCONDITIONS
strain: JW3367 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The txt file includes the gene expression profiles of all the samples. The xlsx file contains the PC1 and PC2 values of all the samples. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into 0.2%(w/v) glucose M9 minimal media. M9 minimal media was also supplemented with 1 ml trace element solution (100X), excluding MG_no_te_1 and MG_no_te_2. The culture was incubated at 37 ℃ overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37 ℃ with agitation to the mid-log phase (OD600 ≈ 0.5). 10mM glutamate was added to the media MG_glu_1 and MG_glu_2. PGCGROWTHCONDITIONS
knock-out: -- PGCGROWTHCONDITIONS
media: M9 minimal media w/ 0.2% glucose w/o trace elements PGCGROWTHCONDITIONS
MG_no_te_1 PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into 0.2%(w/v) glucose M9 minimal media. M9 minimal media was also supplemented with 1 ml trace element solution (100X), excluding MG_no_te_1 and MG_no_te_2. The culture was incubated at 37 ℃ overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37 ℃ with agitation to the mid-log phase (OD600 ≈ 0.5). 10mM glutamate was added to the media MG_glu_1 and MG_glu_2. PGCGROWTHCONDITIONS
knock-out: -- PGCGROWTHCONDITIONS
media: M9 minimal media w/ 0.2% glucose w/o trace elements PGCGROWTHCONDITIONS
MG_no_te_2 PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into 0.2%(w/v) glucose M9 minimal media. M9 minimal media was also supplemented with 1 ml trace element solution (100X), excluding MG_no_te_1 and MG_no_te_2. The culture was incubated at 37 ℃ overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37 ℃ with agitation to the mid-log phase (OD600 ≈ 0.5). 10mM glutamate was added to the media MG_glu_1 and MG_glu_2. PGCGROWTHCONDITIONS
knock-out: -- PGCGROWTHCONDITIONS
media: M9 minimal media w/ 0.2% glucose and 10mM glutamate PGCGROWTHCONDITIONS
MG_glu_1 PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into 0.2%(w/v) glucose M9 minimal media. M9 minimal media was also supplemented with 1 ml trace element solution (100X), excluding MG_no_te_1 and MG_no_te_2. The culture was incubated at 37 ℃ overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37 ℃ with agitation to the mid-log phase (OD600 ≈ 0.5). 10mM glutamate was added to the media MG_glu_1 and MG_glu_2. PGCGROWTHCONDITIONS
knock-out: -- PGCGROWTHCONDITIONS
media: M9 minimal media w/ 0.2% glucose and 10mM glutamate PGCGROWTHCONDITIONS
MG_glu_2 PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into 0.2%(w/v) glucose M9 minimal media. M9 minimal media was also supplemented with 1 ml trace element solution (100X), excluding MG_no_te_1 and MG_no_te_2. The culture was incubated at 37 ℃ overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37 ℃ with agitation to the mid-log phase (OD600 ≈ 0.5). 10mM glutamate was added to the media MG_glu_1 and MG_glu_2. PGCGROWTHCONDITIONS
knock-out: -- PGCGROWTHCONDITIONS
media: M9 minimal media w/ 0.2% glucose PGCGROWTHCONDITIONS
MG_glc PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
wt_glc__1 PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
wt_glc__2 PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
wt_glc__3 PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
wt_glc__4 PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
arg_sbt__1 PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 4g/L D-sorbitol PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
supplement: L-arginine (5.75mM) PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
arg_sbt__2 PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 4g/L D-sorbitol PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
supplement: L-arginine (5.75mM) PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
cytd_rib__1 PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 4g/L D-ribose PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
supplement: Cytidine (1 mM) PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
cytd_rib__2 PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 4g/L D-ribose PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
supplement: Cytidine (1 mM) PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
gth__1 PGCGROWTHCONDITIONS
media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
supplement: glutathione PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
gth__2 PGCGROWTHCONDITIONS
media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
supplement: glutathione PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
leu_glcr__1 PGCGROWTHCONDITIONS
media: M9 minimal media w/ 4g/L glucarate PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
supplement: leucine (10mM) PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
leu_glcr__2 PGCGROWTHCONDITIONS
media: M9 minimal media w/ 4g/L glucarate PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
supplement: leucine (10mM) PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS
met_glc__1 PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
supplement: methionine(5mM) PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS
met_glc__2 PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
supplement: methionine(5mM) PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: anaerobic M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS
no3_anaero__1 PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
supplement: KNO3 (20mM) PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: anaerobic M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS
no3_anaero__2 PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
supplement: KNO3 (20mM) PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 4g/L N-acetylglucosamine PGCGROWTHCONDITIONS
phe_acgam__1 PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
supplement: phenylalanine(5mM) PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 4g/L N-acetylglucosamine PGCGROWTHCONDITIONS
phe_acgam__2 PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
supplement: phenylalanine(5mM) PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 4g/L galactose PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
supplement: thiamine(1uM) PGCGROWTHCONDITIONS
thm_gal__1 PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 4g/L galactose PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
supplement: thiamine(1uM) PGCGROWTHCONDITIONS
thm_gal__2 PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 4g/L D-gluconate PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
supplement: tyrosine(5mM) PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
tyr_glcn__1 PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 4g/L D-gluconate PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
supplement: tyrosine(5mM) PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
tyr_glcn__2 PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 3.3g/L pyruvate PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
supplement: Uracil (1 mM) PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
ura_pyr__1 PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 3.3g/L pyruvate PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
supplement: Uracil (1 mM) PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
ura_pyr__2 PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
wt_glc_5__1 PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
wt_glc_6__1 PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
bw_delpurR_cytd__1 PGCGROWTHCONDITIONS
E. coli BW25113 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 2g/L glucose and 1 mM cytidine PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
bw_delpurR_cytd__2 PGCGROWTHCONDITIONS
E. coli BW25113 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 2g/L glucose and 1 mM cytidine PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
ade_glc__1 PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 2g/L glucose and 100 mg/L adenine PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
ade_glc__2 PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For nitrate respiration cultures, a 35:50 ratio of carbon dioxide to nitrogen was bubbled through hte media to deoxygenate. PGCGROWTHCONDITIONS
media: M9 minimal media w/ 2g/L glucose and 100 mg/L adenine PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with 2g/L glucose, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). PGCGROWTHCONDITIONS
media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS
MG1655_1 PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genomes using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode. Only 1100 genes common across all strains were quantified. PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS
E. coli MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
glycerol stocks of E. coli strains were inoculated into M9 minimal media with 2g/L glucose, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). PGCGROWTHCONDITIONS
media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS
MG1655_2 PGCGROWTHCONDITIONS
Raw sequencing reads were mapped to the reference genomes using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode. Only 1100 genes common across all strains were quantified. PGCGROWTHCONDITIONS
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
At time point 0, rifampicin was added to a final concentration of 500ug/ml. Samples were collected at 0, 2, 4, 6, and 8 minutes. PGCGROWTHCONDITIONS
E.coli strain, DY330, was grown at 30C in M9 media supplemented with 0.4% glucose, vitamins and amino acids. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was purified from lysates by phenol/chloroform method. rRNA was first removed using MICROBExpress following manufacturer’s protocol, except RNA was collected using Zymo’s RNA columns. A second rRNA removal step was performed following the protocol described in Affymetrix Expression Handbook, substituting enzymes MMLV (Ambion), RNase H (NEB), and DnaseI (Amplification grade, Invitrogen). PGCGROWTHCONDITIONS
Sequence reads were obtained and mapped to the W3110 genome (NCBI) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained. Repeated sequences were ignored (rRNA). The counts in each sample was normalized by ssrA RNA and then converted to logarithmic values. A value of 1 was added to every count before the logarithmic conversion to avoid an undefined logarithm of 0. The lifetime was determined from the inverse of the slope of a linear fit to the logarithmic values. PGCGROWTHCONDITIONS
strain: DY330 (W3110) PGCGROWTHCONDITIONS
The measured lifetime of mRNA is available as a supplementary file (real_rna_life.txt) on the Series record. PGCGROWTHCONDITIONS
The RNA was fragmented using Ambion’s Fragmentation Reagent at 70°C for 5 min, and collected by Zymo’s RNA columns. RNA seq libraries were prepared according to Illumna’s protocol, using NEB enzymes and barcoded adapters (Integrated DNA Technologies). The libraries were pooled and sequenced with an Illumina GA II machine (Center for Systems Biology, Harvard University). PGCGROWTHCONDITIONS
time point 0 PGCGROWTHCONDITIONS
treatment group: rifampicin time point 0 PGCGROWTHCONDITIONS
At time point 0, rifampicin was added to a final concentration of 500ug/ml. Samples were collected at 0, 2, 4, 6, and 8 minutes. PGCGROWTHCONDITIONS
E.coli strain, DY330, was grown at 30C in M9 media supplemented with 0.4% glucose, vitamins and amino acids. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was purified from lysates by phenol/chloroform method. rRNA was first removed using MICROBExpress following manufacturer’s protocol, except RNA was collected using Zymo’s RNA columns. A second rRNA removal step was performed following the protocol described in Affymetrix Expression Handbook, substituting enzymes MMLV (Ambion), RNase H (NEB), and DnaseI (Amplification grade, Invitrogen). PGCGROWTHCONDITIONS
Sequence reads were obtained and mapped to the W3110 genome (NCBI) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained. Repeated sequences were ignored (rRNA). The counts in each sample was normalized by ssrA RNA and then converted to logarithmic values. A value of 1 was added to every count before the logarithmic conversion to avoid an undefined logarithm of 0. The lifetime was determined from the inverse of the slope of a linear fit to the logarithmic values. PGCGROWTHCONDITIONS
strain: DY330 (W3110) PGCGROWTHCONDITIONS
The measured lifetime of mRNA is available as a supplementary file (real_rna_life.txt) on the Series record. PGCGROWTHCONDITIONS
The RNA was fragmented using Ambion’s Fragmentation Reagent at 70°C for 5 min, and collected by Zymo’s RNA columns. RNA seq libraries were prepared according to Illumna’s protocol, using NEB enzymes and barcoded adapters (Integrated DNA Technologies). The libraries were pooled and sequenced with an Illumina GA II machine (Center for Systems Biology, Harvard University). PGCGROWTHCONDITIONS
time point 2 PGCGROWTHCONDITIONS
treatment group: rifampicin time point 2 PGCGROWTHCONDITIONS
At time point 0, rifampicin was added to a final concentration of 500ug/ml. Samples were collected at 0, 2, 4, 6, and 8 minutes. PGCGROWTHCONDITIONS
E.coli strain, DY330, was grown at 30C in M9 media supplemented with 0.4% glucose, vitamins and amino acids. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was purified from lysates by phenol/chloroform method. rRNA was first removed using MICROBExpress following manufacturer’s protocol, except RNA was collected using Zymo’s RNA columns. A second rRNA removal step was performed following the protocol described in Affymetrix Expression Handbook, substituting enzymes MMLV (Ambion), RNase H (NEB), and DnaseI (Amplification grade, Invitrogen). PGCGROWTHCONDITIONS
Sequence reads were obtained and mapped to the W3110 genome (NCBI) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained. Repeated sequences were ignored (rRNA). The counts in each sample was normalized by ssrA RNA and then converted to logarithmic values. A value of 1 was added to every count before the logarithmic conversion to avoid an undefined logarithm of 0. The lifetime was determined from the inverse of the slope of a linear fit to the logarithmic values. PGCGROWTHCONDITIONS
strain: DY330 (W3110) PGCGROWTHCONDITIONS
The measured lifetime of mRNA is available as a supplementary file (real_rna_life.txt) on the Series record. PGCGROWTHCONDITIONS
The RNA was fragmented using Ambion’s Fragmentation Reagent at 70°C for 5 min, and collected by Zymo’s RNA columns. RNA seq libraries were prepared according to Illumna’s protocol, using NEB enzymes and barcoded adapters (Integrated DNA Technologies). The libraries were pooled and sequenced with an Illumina GA II machine (Center for Systems Biology, Harvard University). PGCGROWTHCONDITIONS
time point 4 PGCGROWTHCONDITIONS
treatment group: rifampicin time point 4 PGCGROWTHCONDITIONS
At time point 0, rifampicin was added to a final concentration of 500ug/ml. Samples were collected at 0, 2, 4, 6, and 8 minutes. PGCGROWTHCONDITIONS
E.coli strain, DY330, was grown at 30C in M9 media supplemented with 0.4% glucose, vitamins and amino acids. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was purified from lysates by phenol/chloroform method. rRNA was first removed using MICROBExpress following manufacturer’s protocol, except RNA was collected using Zymo’s RNA columns. A second rRNA removal step was performed following the protocol described in Affymetrix Expression Handbook, substituting enzymes MMLV (Ambion), RNase H (NEB), and DnaseI (Amplification grade, Invitrogen). PGCGROWTHCONDITIONS
Sequence reads were obtained and mapped to the W3110 genome (NCBI) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained. Repeated sequences were ignored (rRNA). The counts in each sample was normalized by ssrA RNA and then converted to logarithmic values. A value of 1 was added to every count before the logarithmic conversion to avoid an undefined logarithm of 0. The lifetime was determined from the inverse of the slope of a linear fit to the logarithmic values. PGCGROWTHCONDITIONS
strain: DY330 (W3110) PGCGROWTHCONDITIONS
The measured lifetime of mRNA is available as a supplementary file (real_rna_life.txt) on the Series record. PGCGROWTHCONDITIONS
The RNA was fragmented using Ambion’s Fragmentation Reagent at 70°C for 5 min, and collected by Zymo’s RNA columns. RNA seq libraries were prepared according to Illumna’s protocol, using NEB enzymes and barcoded adapters (Integrated DNA Technologies). The libraries were pooled and sequenced with an Illumina GA II machine (Center for Systems Biology, Harvard University). PGCGROWTHCONDITIONS
time point 6 PGCGROWTHCONDITIONS
treatment group: rifampicin time point 6 PGCGROWTHCONDITIONS
At time point 0, rifampicin was added to a final concentration of 500ug/ml. Samples were collected at 0, 2, 4, 6, and 8 minutes. PGCGROWTHCONDITIONS
E.coli strain, DY330, was grown at 30C in M9 media supplemented with 0.4% glucose, vitamins and amino acids. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was purified from lysates by phenol/chloroform method. rRNA was first removed using MICROBExpress following manufacturer’s protocol, except RNA was collected using Zymo’s RNA columns. A second rRNA removal step was performed following the protocol described in Affymetrix Expression Handbook, substituting enzymes MMLV (Ambion), RNase H (NEB), and DnaseI (Amplification grade, Invitrogen). PGCGROWTHCONDITIONS
Sequence reads were obtained and mapped to the W3110 genome (NCBI) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained. Repeated sequences were ignored (rRNA). The counts in each sample was normalized by ssrA RNA and then converted to logarithmic values. A value of 1 was added to every count before the logarithmic conversion to avoid an undefined logarithm of 0. The lifetime was determined from the inverse of the slope of a linear fit to the logarithmic values. PGCGROWTHCONDITIONS
strain: DY330 (W3110) PGCGROWTHCONDITIONS
The measured lifetime of mRNA is available as a supplementary file (real_rna_life.txt) on the Series record. PGCGROWTHCONDITIONS
The RNA was fragmented using Ambion’s Fragmentation Reagent at 70°C for 5 min, and collected by Zymo’s RNA columns. RNA seq libraries were prepared according to Illumna’s protocol, using NEB enzymes and barcoded adapters (Integrated DNA Technologies). The libraries were pooled and sequenced with an Illumina GA II machine (Center for Systems Biology, Harvard University). PGCGROWTHCONDITIONS
time point 8 PGCGROWTHCONDITIONS
treatment group: rifampicin time point 8 PGCGROWTHCONDITIONS
An overnight culture was diluted to an OD600 of 0.02 in LB media supplemented with 100 µg/ml of carbenicillin, 40 µg/ml biotin, and 70 µM IPTG. The back diluted culture was grown at 37°C until reaching an OD600 of 0.45. PGCGROWTHCONDITIONS
Clarified extracts were treated with microccocal nuclease (45 enzyme units per absorbance unit of lysate at 260 nm), purified through a sucrose cushion, and affinity purified via TF. Ribosome-protected footprints were size selected and converted into a cDNA library for sequencing. PGCGROWTHCONDITIONS
DSP1_AP PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype/variation: MC4100 ∆tig::kan pTig-TEV-Avi PGCGROWTHCONDITIONS
growth stage: mid-log phase PGCGROWTHCONDITIONS
Harvested by chloramphenicol pre-treatment and centrifugation; DSP treated ex vivo; Affinity purified TF crosslinked RNC footprints PGCGROWTHCONDITIONS
library strategy: Selective ribosome profiling PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MC4100 PGCGROWTHCONDITIONS
The .align files have been processed using tagalign. Reads were aligned to the reference genome (Bowtie v.0.12.0) by the first 25 nt and extended to account for the linker. PGCGROWTHCONDITIONS
The culture was incubated with 100 µg/ml of chloramphenicol for 2 min, and harvested by centrifugation. The pellet with washed and resuspended in 100 mM NH4Cl, 10 mM MgCl2, 20 mM Tris Cl, 0.4% Triton X100, 0.1% NP-40, and 100 µl/ml chloramphenicol, and flash frozen over liquid nitrogen. The frozen cell pellets were pulverized by mixer milling and thawed in 2.5 mM DSP. The crosslinking reaction was quenched with 100 mM Tris Cl 8.3. PGCGROWTHCONDITIONS
An overnight culture was diluted to an OD600 of 0.02 in LB media supplemented with 100 µg/ml of carbenicillin, 40 µg/ml biotin, and 70 µM IPTG. The back diluted culture was grown at 37°C until reaching an OD600 of 0.45. PGCGROWTHCONDITIONS
Clarified extracts were treated with microccocal nuclease (45 enzyme units per absorbance unit of lysate at 260 nm), purified through a sucrose gradient. Ribosome-protected footprints were size selected and converted into a cDNA library for sequencing. PGCGROWTHCONDITIONS
DSP1_Total PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype/variation: MC4100 ∆tig::kan pTig-TEV-Avi PGCGROWTHCONDITIONS
growth stage: mid-log phase PGCGROWTHCONDITIONS
Harvested by chloramphenicol pre-treatment and centrifugation; DSP treated ex vivo; Total footprints PGCGROWTHCONDITIONS
library strategy: Ribosome profiling PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MC4100 PGCGROWTHCONDITIONS
The .align files have been processed using tagalign. Reads were aligned to the reference genome (Bowtie v.0.12.0) by the first 25 nt and extended to account for the linker. PGCGROWTHCONDITIONS
The culture was incubated with 100 µg/ml of chloramphenicol for 2 min, and harvested by centrifugation. The pellet with washed and resuspended in 100 mM NH4Cl, 10 mM MgCl2, 20 mM Tris Cl, 0.4% Triton X100, 0.1% NP-40, and 100 µl/ml chloramphenicol, and flash frozen over liquid nitrogen. The frozen cell pellets were pulverized by mixer milling and thawed in 2.5 mM DSP. The crosslinking reaction was quenched with 100 mM Tris Cl 8.3. PGCGROWTHCONDITIONS
An overnight culture was diluted to an OD600 of 0.02 in LB media supplemented with 100 µg/ml of carbenicillin, 40 µg/ml biotin, and 70 µM IPTG. The back diluted culture was grown at 37°C until reaching an OD600 of 0.45. PGCGROWTHCONDITIONS
Clarified extracts were treated with microccocal nuclease (45 enzyme units per absorbance unit of lysate at 260 nm), purified through a sucrose cushion, and affinity purified via TF. Ribosome-protected footprints were size selected and converted into a cDNA library for sequencing. PGCGROWTHCONDITIONS
DSP2_AP PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype/variation: MC4100 ∆tig::kan pTig-TEV-Avi PGCGROWTHCONDITIONS
growth stage: mid-log phase PGCGROWTHCONDITIONS
Harvested by chloramphenicol pre-treatment and centrifugation; DSP treated ex vivo; Affinity purified TF crosslinked RNC footprints PGCGROWTHCONDITIONS
library strategy: Selective ribosome profiling PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MC4100 PGCGROWTHCONDITIONS
The .align files have been processed using tagalign. Reads were aligned to the reference genome (Bowtie v.0.12.0) by the first 25 nt and extended to account for the linker. PGCGROWTHCONDITIONS
The culture was incubated with 100 µg/ml of chloramphenicol for 2 min, and harvested by centrifugation. The pellet with washed and resuspended in 100 mM NH4Cl, 10 mM MgCl2, 20 mM Tris Cl, 0.4% Triton X100, 0.1% NP-40, and 100 µl/ml chloramphenicol, and flash frozen over liquid nitrogen. The frozen cell pellets were pulverized by mixer milling and thawed in 2.5 mM DSP. The crosslinking reaction was quenched with 100 mM Tris Cl 8.3. PGCGROWTHCONDITIONS
An overnight culture was diluted to an OD600 of 0.02 in LB media supplemented with 100 µg/ml of carbenicillin, 40 µg/ml biotin, and 70 µM IPTG. The back diluted culture was grown at 37°C until reaching an OD600 of 0.45. PGCGROWTHCONDITIONS
Clarified extracts were treated with microccocal nuclease (45 enzyme units per absorbance unit of lysate at 260 nm), purified through a sucrose gradient. Ribosome-protected footprints were size selected and converted into a cDNA library for sequencing. PGCGROWTHCONDITIONS
DSP2_Total PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype/variation: MC4100 ∆tig::kan pTig-TEV-Avi PGCGROWTHCONDITIONS
growth stage: mid-log phase PGCGROWTHCONDITIONS
Harvested by chloramphenicol pre-treatment and centrifugation; DSP treated ex vivo; Total footprints PGCGROWTHCONDITIONS
library strategy: Ribosome profiling PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MC4100 PGCGROWTHCONDITIONS
The .align files have been processed using tagalign. Reads were aligned to the reference genome (Bowtie v.0.12.0) by the first 25 nt and extended to account for the linker. PGCGROWTHCONDITIONS
The culture was incubated with 100 µg/ml of chloramphenicol for 2 min, and harvested by centrifugation. The pellet with washed and resuspended in 100 mM NH4Cl, 10 mM MgCl2, 20 mM Tris Cl, 0.4% Triton X100, 0.1% NP-40, and 100 µl/ml chloramphenicol, and flash frozen over liquid nitrogen. The frozen cell pellets were pulverized by mixer milling and thawed in 2.5 mM DSP. The crosslinking reaction was quenched with 100 mM Tris Cl 8.3. PGCGROWTHCONDITIONS
An overnight culture was diluted to an OD600 of 0.02 in LB media supplemented with 100 µg/ml of carbenicillin, 40 µg/ml biotin, and 70 µM IPTG. The back diluted culture was grown at 37°C until reaching an OD600 of 0.45. PGCGROWTHCONDITIONS
Cells were flash frozen in liquid nitrogen after the media was rapidly filtered. Frozen cells were pulverized by mixer milling and thawed in 2.5 mM DSP. The crosslinking reaction was quenched with 100 mM Tris Cl 8.3. PGCGROWTHCONDITIONS
Clarified extracts were treated with microccocal nuclease (45 enzyme units per absorbance unit of lysate at 260 nm), purified through a sucrose cushion, and affinity purified via TF. Ribosome-protected footprints were size selected and converted into a cDNA library for sequencing. PGCGROWTHCONDITIONS
DSP3_AP PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype/variation: MC4100 ∆tig::kan pTig-TEV-Avi PGCGROWTHCONDITIONS
growth stage: mid-log phase PGCGROWTHCONDITIONS
Harvested by rapid filtration; DSP treated ex vivo; Affinity purified TF crosslinked RNC footprints PGCGROWTHCONDITIONS
library strategy: Selective ribosome profiling PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MC4100 PGCGROWTHCONDITIONS
The .align files have been processed using tagalign. Reads were aligned to the reference genome (Bowtie v.0.12.0) by the first 25 nt and extended to account for the linker. PGCGROWTHCONDITIONS
An overnight culture was diluted to an OD600 of 0.02 in LB media supplemented with 100 µg/ml of carbenicillin, 40 µg/ml biotin, and 70 µM IPTG. The back diluted culture was grown at 37°C until reaching an OD600 of 0.45. PGCGROWTHCONDITIONS
Cells were flash frozen in liquid nitrogen after the media was rapidly filtered. Frozen cells were pulverized by mixer milling and thawed in 2.5 mM DSP. The crosslinking reaction was quenched with 100 mM Tris Cl 8.3. PGCGROWTHCONDITIONS
Clarified extracts were treated with microccocal nuclease (45 enzyme units per absorbance unit of lysate at 260 nm), purified through a sucrose gradient. Ribosome-protected footprints were size selected and converted into a cDNA library for sequencing. PGCGROWTHCONDITIONS
DSP3_Total PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype/variation: MC4100 ∆tig::kan pTig-TEV-Avi PGCGROWTHCONDITIONS
growth stage: mid-log phase PGCGROWTHCONDITIONS
Harvested by rapid filtration; DSP treated ex vivo; Total footprints PGCGROWTHCONDITIONS
library strategy: Ribosome profiling PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MC4100 PGCGROWTHCONDITIONS
The .align files have been processed using tagalign. Reads were aligned to the reference genome (Bowtie v.0.12.0) by the first 25 nt and extended to account for the linker. PGCGROWTHCONDITIONS
An overnight culture was diluted to an OD600 of 0.02 in LB media supplemented with 100 µg/ml of carbenicillin, 40 µg/ml biotin, and 70 µM IPTG. The back diluted culture was grown at 37°C until reaching an OD600 of 0.45. PGCGROWTHCONDITIONS
Cells were flash frozen in liquid nitrogen after the media was rapidly filtered. Frozen cells were pulverized by mixer milling and thawed in 20 mM EDC, pH 5.8. The crosslinking reaction was quenched with 250 mM glycine, 100 mM Tris Cl 8.0, and 4 mM NaHCO3. PGCGROWTHCONDITIONS
Clarified extracts were treated with microccocal nuclease (45 enzyme units per absorbance unit of lysate at 260 nm), purified through a sucrose cushion, and affinity purified via TF. Ribosome-protected footprints were size selected and converted into a cDNA library for sequencing. PGCGROWTHCONDITIONS
EDC1_AP PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype/variation: MC4100 ∆tig::kan pTig-TEV-Avi PGCGROWTHCONDITIONS
growth stage: mid-log phase PGCGROWTHCONDITIONS
Harvested by rapid filtration; EDC treated ex vivo; Affinity purified TF crosslinked RNC footprints PGCGROWTHCONDITIONS
library strategy: Selective ribosome profiling PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MC4100 PGCGROWTHCONDITIONS
The .align files have been processed using tagalign. Reads were aligned to the reference genome (Bowtie v.0.12.0) by the first 25 nt and extended to account for the linker. PGCGROWTHCONDITIONS
An overnight culture was diluted to an OD600 of 0.02 in LB media supplemented with 100 µg/ml of carbenicillin, 40 µg/ml biotin, and 70 µM IPTG. The back diluted culture was grown at 37°C until reaching an OD600 of 0.45. PGCGROWTHCONDITIONS
Cells were flash frozen in liquid nitrogen after the media was rapidly filtered. Frozen cells were pulverized by mixer milling and thawed in 20 mM EDC, pH 5.8. The crosslinking reaction was quenched with 250 mM glycine, 100 mM Tris Cl 8.0, and 4 mM NaHCO3. PGCGROWTHCONDITIONS
Clarified extracts were treated with microccocal nuclease (45 enzyme units per absorbance unit of lysate at 260 nm), purified through a sucrose gradient. Ribosome-protected footprints were size selected and converted into a cDNA library for sequencing. PGCGROWTHCONDITIONS
EDC1_Total PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype/variation: MC4100 ∆tig::kan pTig-TEV-Avi PGCGROWTHCONDITIONS
growth stage: mid-log phase PGCGROWTHCONDITIONS
Harvested by rapid filtration; EDC treated ex vivo; Total footprints PGCGROWTHCONDITIONS
library strategy: Ribosome profiling PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: MC4100 PGCGROWTHCONDITIONS
The .align files have been processed using tagalign. Reads were aligned to the reference genome (Bowtie v.0.12.0) by the first 25 nt and extended to account for the linker. PGCGROWTHCONDITIONS
E. coli [K-12 MG1655 strain (U00096.2)] was grown overnight at 30 °C in LB medium.  The resulting culture was diluted 500-fold in fresh LB medium and grown at 30 °C for 3.5 hours such that O.D. at 600 nm became 0.30-0.35. PGCGROWTHCONDITIONS
E_coli_transcriptome_2 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome build: E. coli [K-12 MG1655 strain (U00096.2) PGCGROWTHCONDITIONS
genotype: F-, lambda-, rph-1 PGCGROWTHCONDITIONS
reference genome: U00096.2 PGCGROWTHCONDITIONS
RNA from Escherichia coli PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was purified by a standard protocol using Phenol Chloroform.  Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria) (Epicentre, Illumina).  Then, the conventional Illumina protocol for mRNA Sequencing Sample Preparation was applied with a few modifications (see original paper). PGCGROWTHCONDITIONS
Standard Paired-End Illumina Library Construction Protocol was used with modified adapters containing optimized 20 bp barcode sequences (see original paper).  Samples with barcoded adapters were sequenced on an Illumina HiSeq 2000 with a 2x101 (for the first sequencing run) and 2x51 (for the second) base paired-end reads in one lane. PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Using a combination of python (3.2.1) and bowtie(0.12.7), from the raw sequencing data, we isolated reads which contained barcode sequences that corresponded to our original list of single molecule barcodes in both forward and reverse reads for each sequence pair that had at most one mismatch. We then aligned the first 28 bases (26 bases for the second sequencing run) of the targeted sequence of both the forward and reverse reads of each cluster to the E. coli genome and kept the sequences that uniquely align fewer than three mismatches and where the two reads did not map to the same sense or antisense strand of the genome.  We used a detailed filtering process to determine the identity of closely-mapped reads. Mapped sequence fragments with a length of at least 1,000 bases were discarded.  All sequences within the same transcription unit that had the same unique tag were analyzed further. We determined that more than one sequence with the same unique tag were identical if the distance between their center positions was less than four base-pairs and if the difference in length was less than 9 base-pairs. Then for each unique sequence, we counted the number of unique barcode tags that appeared to determine the copy number of each sequence and mapped each of them to genes. We include indexed genome viewer files (.sam and .sai) for both experiments using both the conventional method and the digital method. PGCGROWTHCONDITIONS
After each sequenced fragments were aligned to the reference genome using Bowtie, the position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 12 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. More at G.W. Li, E. Oh, and J.S. Weissman, Nature (in press) PGCGROWTHCONDITIONS
E. coli recoded ompF (recoded ompF gene) PGCGROWTHCONDITIONS
E. coli recoded ompF PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome Build: PGCGROWTHCONDITIONS
medium: MOPS PGCGROWTHCONDITIONS
OmpFrecode_f.wig: NC_000913.2 PGCGROWTHCONDITIONS
OmpFrecode_r.wig: NC_000913.2 PGCGROWTHCONDITIONS
Ribosome protected mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More at G.W. Li, E. Oh, and J.S. Weissman, Nature (in press) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: BJW9 w/ recoded ompF PGCGROWTHCONDITIONS
treatment: Ribosome-protected mRNA, Ribosome footprint sample digested with 60 units of micrococcal nuclease per A260 absorbance PGCGROWTHCONDITIONS
bacteria grown at 37° C with shaking until log phase PGCGROWTHCONDITIONS
cDNA reads were trimmed so that the quality at each base position was above 30 (~15-20 bp) and then mapped either to the E. coli K-12 MG1655 published genome sequence (Genbank accession no. NC_000913) or to the pAR060302 published sequence (Genbank accession no. NC_092692) using BOWTIE.  The E. coli strain DH5α has an incomplete annotation and for this reason the E. coli K-12 annotation was used, representing an estimation of differentially expressed genes due to exposure of antimicrobials.  Mapped reads for 3 seperate sequencing runs were combined because some sequencing runs were not fully completed due to technical difficulties.  For each condition, graphs representing the number of mapped reads per nucleotide were generated and visualized using the Integrated Genome Viewer (IGV).  Images were created using XplasMap (http://www.iayork.com/XPlasMap/) and IGV.  The reads mapped per kilobase of gene per million (RPKM) reads was calculated using either the E. coli chromosome or the pAR060302 annotation and was used for global normalization.  The per kilobase cDNA length normalized the effect of different length of cDNAs such that the sequence reads have a equal chance to map on the long cDNA regions and the short cDNA regions.  After RPKM normalization, each sample is comparable to each other.  An R package, DEGseq , was used to identify differentially expressed genes between the control and each antibiotic treatment condition. PGCGROWTHCONDITIONS
Cells were pelleted and RNA was purified using a commercially available RNA extraction kit (Qiagen).  RNA preparations were then subjected to a DNase treatment to eliminate DNA contamination from the sample (Qiagen).  A treatment was also included to deplete ribosomal RNA using a commercially available kit (MicrobExpress, Ambion).  The two biological replicates for each growth condition were pooled for sequencing. PGCGROWTHCONDITIONS
E. coli strain DH5α harboring pAR060302 was grown in 10 mL DifcoTM Luria-Bertani (LB) broth aliquots at 37º C with shaking until an OD600 of 0.5. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
no treatment PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: DH5α(pAR060302) PGCGROWTHCONDITIONS
treatment: none PGCGROWTHCONDITIONS
bacteria grown at 37° C with shaking until log phase with florfenicol treatment PGCGROWTHCONDITIONS
cDNA reads were trimmed so that the quality at each base position was above 30 (~15-20 bp) and then mapped either to the E. coli K-12 MG1655 published genome sequence (Genbank accession no. NC_000913) or to the pAR060302 published sequence (Genbank accession no. NC_092692) using BOWTIE.  The E. coli strain DH5α has an incomplete annotation and for this reason the E. coli K-12 annotation was used, representing an estimation of differentially expressed genes due to exposure of antimicrobials.  Mapped reads for 3 seperate sequencing runs were combined because some sequencing runs were not fully completed due to technical difficulties.  For each condition, graphs representing the number of mapped reads per nucleotide were generated and visualized using the Integrated Genome Viewer (IGV).  Images were created using XplasMap (http://www.iayork.com/XPlasMap/) and IGV.  The reads mapped per kilobase of gene per million (RPKM) reads was calculated using either the E. coli chromosome or the pAR060302 annotation and was used for global normalization.  The per kilobase cDNA length normalized the effect of different length of cDNAs such that the sequence reads have a equal chance to map on the long cDNA regions and the short cDNA regions.  After RPKM normalization, each sample is comparable to each other.  An R package, DEGseq , was used to identify differentially expressed genes between the control and each antibiotic treatment condition. PGCGROWTHCONDITIONS
Cells were pelleted and RNA was purified using a commercially available RNA extraction kit (Qiagen).  RNA preparations were then subjected to a DNase treatment to eliminate DNA contamination from the sample (Qiagen).  A treatment was also included to deplete ribosomal RNA using a commercially available kit (MicrobExpress, Ambion).  The two biological replicates for each growth condition were pooled for sequencing. PGCGROWTHCONDITIONS
E. coli strain DH5α harboring pAR060302 was grown in 10 mL DifcoTM Luria-Bertani (LB) broth aliquots at 37º C with shaking until an OD600 of 0.5. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Florfenicol_treatment_plasmidmappedreads_statistical_output.txt: NC_012692.1 PGCGROWTHCONDITIONS
florfenicol treatment PGCGROWTHCONDITIONS
Flor_treatment_genomemappedreads_statistical_output.txt: NC_000913.2 PGCGROWTHCONDITIONS
Genome Build: PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: DH5α(pAR060302) PGCGROWTHCONDITIONS
treatment: florfenicol (30 µg/mL final concentration) PGCGROWTHCONDITIONS
Ampicilin_treatment_plasmidmappedreads_statistical_output.txt: NC_012692.1 PGCGROWTHCONDITIONS
ampicilin treatment PGCGROWTHCONDITIONS
Amp_Treatment_genomemappedreads_statistical_output.txt: NC_000913.2 PGCGROWTHCONDITIONS
bacteria grown at 37° C with shaking until log phase with ampicilin treatment PGCGROWTHCONDITIONS
cDNA reads were trimmed so that the quality at each base position was above 30 (~15-20 bp) and then mapped either to the E. coli K-12 MG1655 published genome sequence (Genbank accession no. NC_000913) or to the pAR060302 published sequence (Genbank accession no. NC_092692) using BOWTIE.  The E. coli strain DH5α has an incomplete annotation and for this reason the E. coli K-12 annotation was used, representing an estimation of differentially expressed genes due to exposure of antimicrobials.  Mapped reads for 3 seperate sequencing runs were combined because some sequencing runs were not fully completed due to technical difficulties.  For each condition, graphs representing the number of mapped reads per nucleotide were generated and visualized using the Integrated Genome Viewer (IGV).  Images were created using XplasMap (http://www.iayork.com/XPlasMap/) and IGV.  The reads mapped per kilobase of gene per million (RPKM) reads was calculated using either the E. coli chromosome or the pAR060302 annotation and was used for global normalization.  The per kilobase cDNA length normalized the effect of different length of cDNAs such that the sequence reads have a equal chance to map on the long cDNA regions and the short cDNA regions.  After RPKM normalization, each sample is comparable to each other.  An R package, DEGseq , was used to identify differentially expressed genes between the control and each antibiotic treatment condition. PGCGROWTHCONDITIONS
Cells were pelleted and RNA was purified using a commercially available RNA extraction kit (Qiagen).  RNA preparations were then subjected to a DNase treatment to eliminate DNA contamination from the sample (Qiagen).  A treatment was also included to deplete ribosomal RNA using a commercially available kit (MicrobExpress, Ambion).  The two biological replicates for each growth condition were pooled for sequencing. PGCGROWTHCONDITIONS
E. coli strain DH5α harboring pAR060302 was grown in 10 mL DifcoTM Luria-Bertani (LB) broth aliquots at 37º C with shaking until an OD600 of 0.5. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome Build: PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: DH5α(pAR060302) PGCGROWTHCONDITIONS
treatment: ampicillin (50 µg/mL final concentration) PGCGROWTHCONDITIONS
bacteria grown at 37° C with shaking until log phase with streptomycin treatment PGCGROWTHCONDITIONS
cDNA reads were trimmed so that the quality at each base position was above 30 (~15-20 bp) and then mapped either to the E. coli K-12 MG1655 published genome sequence (Genbank accession no. NC_000913) or to the pAR060302 published sequence (Genbank accession no. NC_092692) using BOWTIE.  The E. coli strain DH5α has an incomplete annotation and for this reason the E. coli K-12 annotation was used, representing an estimation of differentially expressed genes due to exposure of antimicrobials.  Mapped reads for 3 seperate sequencing runs were combined because some sequencing runs were not fully completed due to technical difficulties.  For each condition, graphs representing the number of mapped reads per nucleotide were generated and visualized using the Integrated Genome Viewer (IGV).  Images were created using XplasMap (http://www.iayork.com/XPlasMap/) and IGV.  The reads mapped per kilobase of gene per million (RPKM) reads was calculated using either the E. coli chromosome or the pAR060302 annotation and was used for global normalization.  The per kilobase cDNA length normalized the effect of different length of cDNAs such that the sequence reads have a equal chance to map on the long cDNA regions and the short cDNA regions.  After RPKM normalization, each sample is comparable to each other.  An R package, DEGseq , was used to identify differentially expressed genes between the control and each antibiotic treatment condition. PGCGROWTHCONDITIONS
Cells were pelleted and RNA was purified using a commercially available RNA extraction kit (Qiagen).  RNA preparations were then subjected to a DNase treatment to eliminate DNA contamination from the sample (Qiagen).  A treatment was also included to deplete ribosomal RNA using a commercially available kit (MicrobExpress, Ambion).  The two biological replicates for each growth condition were pooled for sequencing. PGCGROWTHCONDITIONS
E. coli strain DH5α harboring pAR060302 was grown in 10 mL DifcoTM Luria-Bertani (LB) broth aliquots at 37º C with shaking until an OD600 of 0.5. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome Build: PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: DH5α(pAR060302) PGCGROWTHCONDITIONS
Streptomycin_treatment_plasmidmappedreads_statistical_output.txt: NC_012692.1 PGCGROWTHCONDITIONS
streptomycin treatment PGCGROWTHCONDITIONS
Strep_treatment_genomemappedreads_statistical_output.txt: NC_000913.2 PGCGROWTHCONDITIONS
treatment: streptomycin (50 µg/mL final concentration) PGCGROWTHCONDITIONS
1mL aliquots were harvested and mixed with 0.5mL Phenol/ethanol (5% (v/v) Phenol in EtOHabs). Cells were collected by centrifugation and stored at -80°C until use. PGCGROWTHCONDITIONS
Bacterial cell PGCGROWTHCONDITIONS
biological replicate: 1 PGCGROWTHCONDITIONS
Clones were grown in M9 with 0.4% (w/v) glucose as carbon source minimal medium with 0.3M NaCl (osmotic stress medium) to mid-log phase (OD600 approx. 0.8). PGCGROWTHCONDITIONS
Differentially expressed (DE) genes in all stress evolved strains were found relative to the expression levels in the reference G500 strain using the edgeR R package. PGCGROWTHCONDITIONS
Differentially expressed genes were identified by processing raw counts of mapped reads with edgeR R library version 2.6.9. Normalized counts for each biological replicate were averaged between two technical replicates. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
G500_1 PGCGROWTHCONDITIONS
Genes from the amplified regions in O500 (12-fold) and P500 (two-fold) strains are significantly over-expressed relative to the reference: average log Fold Change for concentrations is +3.6 and +0.8 (both with p-values<10-20), respectively. PGCGROWTHCONDITIONS
Genes with BH (Benjamini and Hochberg) adjusted p-values below 0.05 threshold were selected as DE genes. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli strain K12 sub-strain MG1655 genome (GenBank accession no. U00096.2) PGCGROWTHCONDITIONS
Illumina GAII reads were filtered by SGA version 0.9.9 with the following options: sga preprocess -q 10 -f 10 -m 25 (quality trim 10, quality filter 10, minimal length 25) PGCGROWTHCONDITIONS
preprocessed RNA-Seq reads were mapped to the reference Escherichia coli strain K12 sub-strain MG1655 genome (GenBank accession no. U00096.2) by BWA toolkit version 0.5.9-r16 with the following options: bwa aln -q 20 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using an RNeasy kit (Qiagen) and after 1st and 2nd strand cDNA synthesis, linker ligation and size selection subjected to shotgun sequencing using single read 40bp read length runs on an Illumina Genome Analyzer GAII. PGCGROWTHCONDITIONS
strain: MG 1655 PGCGROWTHCONDITIONS
stress: Minimal medium PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text file; includes: gene differential expression levels relative to the G500 strain with corresponding p-values and processed counts for each biological replicate (each normolized and averaged between 2 technical replicates).  Linked as supplementary file on Series record. PGCGROWTHCONDITIONS
technical replicates: 2 PGCGROWTHCONDITIONS
1mL aliquots were harvested and mixed with 0.5mL Phenol/ethanol (5% (v/v) Phenol in EtOHabs). Cells were collected by centrifugation and stored at -80°C until use. PGCGROWTHCONDITIONS
B500_1 PGCGROWTHCONDITIONS
Bacterial cell PGCGROWTHCONDITIONS
biological replicate: 1 PGCGROWTHCONDITIONS
Clones were grown in M9 with 0.4% (w/v) glucose as carbon source minimal medium with 0.3M NaCl (osmotic stress medium) to mid-log phase (OD600 approx. 0.8). PGCGROWTHCONDITIONS
Differentially expressed (DE) genes in all stress evolved strains were found relative to the expression levels in the reference G500 strain using the edgeR R package. PGCGROWTHCONDITIONS
Differentially expressed genes were identified by processing raw counts of mapped reads with edgeR R library version 2.6.9. Normalized counts for each biological replicate were averaged between two technical replicates. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genes from the amplified regions in O500 (12-fold) and P500 (two-fold) strains are significantly over-expressed relative to the reference: average log Fold Change for concentrations is +3.6 and +0.8 (both with p-values<10-20), respectively. PGCGROWTHCONDITIONS
Genes with BH (Benjamini and Hochberg) adjusted p-values below 0.05 threshold were selected as DE genes. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli strain K12 sub-strain MG1655 genome (GenBank accession no. U00096.2) PGCGROWTHCONDITIONS
Illumina GAII reads were filtered by SGA version 0.9.9 with the following options: sga preprocess -q 10 -f 10 -m 25 (quality trim 10, quality filter 10, minimal length 25) PGCGROWTHCONDITIONS
preprocessed RNA-Seq reads were mapped to the reference Escherichia coli strain K12 sub-strain MG1655 genome (GenBank accession no. U00096.2) by BWA toolkit version 0.5.9-r16 with the following options: bwa aln -q 20 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using an RNeasy kit (Qiagen) and after 1st and 2nd strand cDNA synthesis, linker ligation and size selection subjected to shotgun sequencing using single read 40bp read length runs on an Illumina Genome Analyzer GAII. PGCGROWTHCONDITIONS
strain: MG 1655 PGCGROWTHCONDITIONS
stress: n-butanol PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text file; includes: gene differential expression levels relative to the G500 strain with corresponding p-values and processed counts for each biological replicate (each normolized and averaged between 2 technical replicates).  Linked as supplementary file on Series record. PGCGROWTHCONDITIONS
technical replicates: 2 PGCGROWTHCONDITIONS
1mL aliquots were harvested and mixed with 0.5mL Phenol/ethanol (5% (v/v) Phenol in EtOHabs). Cells were collected by centrifugation and stored at -80°C until use. PGCGROWTHCONDITIONS
Bacterial cell PGCGROWTHCONDITIONS
biological replicate: 1 PGCGROWTHCONDITIONS
Clones were grown in M9 with 0.4% (w/v) glucose as carbon source minimal medium with 0.3M NaCl (osmotic stress medium) to mid-log phase (OD600 approx. 0.8). PGCGROWTHCONDITIONS
Differentially expressed (DE) genes in all stress evolved strains were found relative to the expression levels in the reference G500 strain using the edgeR R package. PGCGROWTHCONDITIONS
Differentially expressed genes were identified by processing raw counts of mapped reads with edgeR R library version 2.6.9. Normalized counts for each biological replicate were averaged between two technical replicates. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genes from the amplified regions in O500 (12-fold) and P500 (two-fold) strains are significantly over-expressed relative to the reference: average log Fold Change for concentrations is +3.6 and +0.8 (both with p-values<10-20), respectively. PGCGROWTHCONDITIONS
Genes with BH (Benjamini and Hochberg) adjusted p-values below 0.05 threshold were selected as DE genes. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli strain K12 sub-strain MG1655 genome (GenBank accession no. U00096.2) PGCGROWTHCONDITIONS
H500_1 PGCGROWTHCONDITIONS
Illumina GAII reads were filtered by SGA version 0.9.9 with the following options: sga preprocess -q 10 -f 10 -m 25 (quality trim 10, quality filter 10, minimal length 25) PGCGROWTHCONDITIONS
preprocessed RNA-Seq reads were mapped to the reference Escherichia coli strain K12 sub-strain MG1655 genome (GenBank accession no. U00096.2) by BWA toolkit version 0.5.9-r16 with the following options: bwa aln -q 20 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using an RNeasy kit (Qiagen) and after 1st and 2nd strand cDNA synthesis, linker ligation and size selection subjected to shotgun sequencing using single read 40bp read length runs on an Illumina Genome Analyzer GAII. PGCGROWTHCONDITIONS
strain: MG 1655 PGCGROWTHCONDITIONS
stress: oxidative PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text file; includes: gene differential expression levels relative to the G500 strain with corresponding p-values and processed counts for each biological replicate (each normolized and averaged between 2 technical replicates).  Linked as supplementary file on Series record. PGCGROWTHCONDITIONS
technical replicates: 2 PGCGROWTHCONDITIONS
1mL aliquots were harvested and mixed with 0.5mL Phenol/ethanol (5% (v/v) Phenol in EtOHabs). Cells were collected by centrifugation and stored at -80°C until use. PGCGROWTHCONDITIONS
Bacterial cell PGCGROWTHCONDITIONS
biological replicate: 1 PGCGROWTHCONDITIONS
Clones were grown in M9 with 0.4% (w/v) glucose as carbon source minimal medium with 0.3M NaCl (osmotic stress medium) to mid-log phase (OD600 approx. 0.8). PGCGROWTHCONDITIONS
Differentially expressed (DE) genes in all stress evolved strains were found relative to the expression levels in the reference G500 strain using the edgeR R package. PGCGROWTHCONDITIONS
Differentially expressed genes were identified by processing raw counts of mapped reads with edgeR R library version 2.6.9. Normalized counts for each biological replicate were averaged between two technical replicates. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genes from the amplified regions in O500 (12-fold) and P500 (two-fold) strains are significantly over-expressed relative to the reference: average log Fold Change for concentrations is +3.6 and +0.8 (both with p-values<10-20), respectively. PGCGROWTHCONDITIONS
Genes with BH (Benjamini and Hochberg) adjusted p-values below 0.05 threshold were selected as DE genes. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli strain K12 sub-strain MG1655 genome (GenBank accession no. U00096.2) PGCGROWTHCONDITIONS
Illumina GAII reads were filtered by SGA version 0.9.9 with the following options: sga preprocess -q 10 -f 10 -m 25 (quality trim 10, quality filter 10, minimal length 25) PGCGROWTHCONDITIONS
O500_1 PGCGROWTHCONDITIONS
preprocessed RNA-Seq reads were mapped to the reference Escherichia coli strain K12 sub-strain MG1655 genome (GenBank accession no. U00096.2) by BWA toolkit version 0.5.9-r16 with the following options: bwa aln -q 20 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using an RNeasy kit (Qiagen) and after 1st and 2nd strand cDNA synthesis, linker ligation and size selection subjected to shotgun sequencing using single read 40bp read length runs on an Illumina Genome Analyzer GAII. PGCGROWTHCONDITIONS
strain: MG 1655 PGCGROWTHCONDITIONS
stress: osmotic PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text file; includes: gene differential expression levels relative to the G500 strain with corresponding p-values and processed counts for each biological replicate (each normolized and averaged between 2 technical replicates).  Linked as supplementary file on Series record. PGCGROWTHCONDITIONS
technical replicates: 2 PGCGROWTHCONDITIONS
1mL aliquots were harvested and mixed with 0.5mL Phenol/ethanol (5% (v/v) Phenol in EtOHabs). Cells were collected by centrifugation and stored at -80°C until use. PGCGROWTHCONDITIONS
Bacterial cell PGCGROWTHCONDITIONS
biological replicate: 2 PGCGROWTHCONDITIONS
Clones were grown in M9 with 0.4% (w/v) glucose as carbon source minimal medium with 0.3M NaCl (osmotic stress medium) to mid-log phase (OD600 approx. 0.8). PGCGROWTHCONDITIONS
Differentially expressed (DE) genes in all stress evolved strains were found relative to the expression levels in the reference G500 strain using the edgeR R package. PGCGROWTHCONDITIONS
Differentially expressed genes were identified by processing raw counts of mapped reads with edgeR R library version 2.6.9. Normalized counts for each biological replicate were averaged between two technical replicates. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genes from the amplified regions in O500 (12-fold) and P500 (two-fold) strains are significantly over-expressed relative to the reference: average log Fold Change for concentrations is +3.6 and +0.8 (both with p-values<10-20), respectively. PGCGROWTHCONDITIONS
Genes with BH (Benjamini and Hochberg) adjusted p-values below 0.05 threshold were selected as DE genes. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli strain K12 sub-strain MG1655 genome (GenBank accession no. U00096.2) PGCGROWTHCONDITIONS
Illumina GAII reads were filtered by SGA version 0.9.9 with the following options: sga preprocess -q 10 -f 10 -m 25 (quality trim 10, quality filter 10, minimal length 25) PGCGROWTHCONDITIONS
O500_2 PGCGROWTHCONDITIONS
preprocessed RNA-Seq reads were mapped to the reference Escherichia coli strain K12 sub-strain MG1655 genome (GenBank accession no. U00096.2) by BWA toolkit version 0.5.9-r16 with the following options: bwa aln -q 20 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using an RNeasy kit (Qiagen) and after 1st and 2nd strand cDNA synthesis, linker ligation and size selection subjected to shotgun sequencing using single read 40bp read length runs on an Illumina Genome Analyzer GAII. PGCGROWTHCONDITIONS
strain: MG 1655 PGCGROWTHCONDITIONS
stress: osmotic PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text file; includes: gene differential expression levels relative to the G500 strain with corresponding p-values and processed counts for each biological replicate (each normolized and averaged between 2 technical replicates).  Linked as supplementary file on Series record. PGCGROWTHCONDITIONS
technical replicates: 2 PGCGROWTHCONDITIONS
1mL aliquots were harvested and mixed with 0.5mL Phenol/ethanol (5% (v/v) Phenol in EtOHabs). Cells were collected by centrifugation and stored at -80°C until use. PGCGROWTHCONDITIONS
Bacterial cell PGCGROWTHCONDITIONS
biological replicate: 1 PGCGROWTHCONDITIONS
Clones were grown in M9 with 0.4% (w/v) glucose as carbon source minimal medium with 0.3M NaCl (osmotic stress medium) to mid-log phase (OD600 approx. 0.8). PGCGROWTHCONDITIONS
Differentially expressed (DE) genes in all stress evolved strains were found relative to the expression levels in the reference G500 strain using the edgeR R package. PGCGROWTHCONDITIONS
Differentially expressed genes were identified by processing raw counts of mapped reads with edgeR R library version 2.6.9. Normalized counts for each biological replicate were averaged between two technical replicates. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genes from the amplified regions in O500 (12-fold) and P500 (two-fold) strains are significantly over-expressed relative to the reference: average log Fold Change for concentrations is +3.6 and +0.8 (both with p-values<10-20), respectively. PGCGROWTHCONDITIONS
Genes with BH (Benjamini and Hochberg) adjusted p-values below 0.05 threshold were selected as DE genes. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli strain K12 sub-strain MG1655 genome (GenBank accession no. U00096.2) PGCGROWTHCONDITIONS
Illumina GAII reads were filtered by SGA version 0.9.9 with the following options: sga preprocess -q 10 -f 10 -m 25 (quality trim 10, quality filter 10, minimal length 25) PGCGROWTHCONDITIONS
P500_1 PGCGROWTHCONDITIONS
preprocessed RNA-Seq reads were mapped to the reference Escherichia coli strain K12 sub-strain MG1655 genome (GenBank accession no. U00096.2) by BWA toolkit version 0.5.9-r16 with the following options: bwa aln -q 20 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using an RNeasy kit (Qiagen) and after 1st and 2nd strand cDNA synthesis, linker ligation and size selection subjected to shotgun sequencing using single read 40bp read length runs on an Illumina Genome Analyzer GAII. PGCGROWTHCONDITIONS
strain: MG 1655 PGCGROWTHCONDITIONS
stress: acidic PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text file; includes: gene differential expression levels relative to the G500 strain with corresponding p-values and processed counts for each biological replicate (each normolized and averaged between 2 technical replicates).  Linked as supplementary file on Series record. PGCGROWTHCONDITIONS
technical replicates: 2 PGCGROWTHCONDITIONS
Base calling was performed by the DOE Joint Genome Institute using Illumina software. PGCGROWTHCONDITIONS
Cells were grown in MOPS minimal medium with 0.2% glucose at 37 oC  in gas-sparged Roux bottles or shaking flasks to mid-log phase (OD600 ~ 0.3-0.4). PGCGROWTHCONDITIONS
Counts per million unique reads were calculated for each gene. PGCGROWTHCONDITIONS
Cultures were transferred directly into an ice-cold ethanol/phenol stop solution, which immediately inactivated cellular RNases. Cells were collected by centrifugation and stored at -80 oC until RNA extraction. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genome_build: U00096.2 PGCGROWTHCONDITIONS
genotype/variation: wild-type PGCGROWTHCONDITIONS
MG1655 1 PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: ribosome-depeleted RNA PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-Seq was performed by the DOE Joint Genome Institute using the dUTP method. Briefly, ribosome-depleted RNA was fragmented in a buffered zinc solution, then purified using AMPure SPRI beads. First-strand cDNAs were then synthesized from the fragmented RNA using Superscript II reverse transcriptase, followed by a second bead purification. dUTP was included in the second strand synthesis reaction in addition to dTTP to chemically mark the second strand.  Two further bead purification steps using different ratios of beads to cDNA (85/100, then 140/100) selected cDNAs in a range between 150-350 bp. cDNAs were then A-tailed using Exo- Klenow, followed by ligation of sequencing adapter oligos. Following bead purification, dUTP was cleaved from the second strand using AmpErase Uracil N-glycosylase, resulting in adaptor ligated single stranded cDNAs. PGCGROWTHCONDITIONS
Sequenced reads were trimmed, the mapped to the Escherichia coli K-12 MG1655 genome (U00096.2) using SOAP. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample PGCGROWTHCONDITIONS
Total RNA was extracted from cell pellets by hot phenol extraction. The integrity of total RNA was determined from agarose gel or microchannel electrophoretograms. 16S and 23S Ribosomal RNA was depleted prior to construction of RNAseq libraries using MICROBExpress reagents. PGCGROWTHCONDITIONS
Base calling was performed by the DOE Joint Genome Institute using Illumina software. PGCGROWTHCONDITIONS
Cells were grown in MOPS minimal medium with 0.2% glucose at 37 oC  in gas-sparged Roux bottles or shaking flasks to mid-log phase (OD600 ~ 0.3-0.4). PGCGROWTHCONDITIONS
Counts per million unique reads were calculated for each gene. PGCGROWTHCONDITIONS
Cultures were transferred directly into an ice-cold ethanol/phenol stop solution, which immediately inactivated cellular RNases. Cells were collected by centrifugation and stored at -80 oC until RNA extraction. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genome_build: U00096.2 PGCGROWTHCONDITIONS
genotype/variation: wild-type PGCGROWTHCONDITIONS
MG1655 2 PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
molecule subtype: ribosome-depeleted RNA PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-Seq was performed by the DOE Joint Genome Institute using the dUTP method. Briefly, ribosome-depleted RNA was fragmented in a buffered zinc solution, then purified using AMPure SPRI beads. First-strand cDNAs were then synthesized from the fragmented RNA using Superscript II reverse transcriptase, followed by a second bead purification. dUTP was included in the second strand synthesis reaction in addition to dTTP to chemically mark the second strand.  Two further bead purification steps using different ratios of beads to cDNA (85/100, then 140/100) selected cDNAs in a range between 150-350 bp. cDNAs were then A-tailed using Exo- Klenow, followed by ligation of sequencing adapter oligos. Following bead purification, dUTP was cleaved from the second strand using AmpErase Uracil N-glycosylase, resulting in adaptor ligated single stranded cDNAs. PGCGROWTHCONDITIONS
Sequenced reads were trimmed, the mapped to the Escherichia coli K-12 MG1655 genome (U00096.2) using SOAP. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample PGCGROWTHCONDITIONS
Total RNA was extracted from cell pellets by hot phenol extraction. The integrity of total RNA was determined from agarose gel or microchannel electrophoretograms. 16S and 23S Ribosomal RNA was depleted prior to construction of RNAseq libraries using MICROBExpress reagents. PGCGROWTHCONDITIONS
Base calling was performed by the DOE Joint Genome Institute using Illumina software. PGCGROWTHCONDITIONS
Cells were grown in MOPS minimal medium with 0.2% glucose at 37 oC  in gas-sparged Roux bottles or shaking flasks to mid-log phase (OD600 ~ 0.3-0.4). PGCGROWTHCONDITIONS
Counts per million unique reads were calculated for each gene. PGCGROWTHCONDITIONS
Cultures were transferred directly into an ice-cold ethanol/phenol stop solution, which immediately inactivated cellular RNases. Cells were collected by centrifugation and stored at -80 oC until RNA extraction. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genome_build: U00096.2 PGCGROWTHCONDITIONS
genotype/variation: wild-type PGCGROWTHCONDITIONS
MG1655 + 20 ug/ml bicyclomycin 1 PGCGROWTHCONDITIONS
MG1655 + 20 ug/ml bicyclomycin PGCGROWTHCONDITIONS
molecule subtype: ribosome-depeleted RNA PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-Seq was performed by the DOE Joint Genome Institute using the dUTP method. Briefly, ribosome-depleted RNA was fragmented in a buffered zinc solution, then purified using AMPure SPRI beads. First-strand cDNAs were then synthesized from the fragmented RNA using Superscript II reverse transcriptase, followed by a second bead purification. dUTP was included in the second strand synthesis reaction in addition to dTTP to chemically mark the second strand.  Two further bead purification steps using different ratios of beads to cDNA (85/100, then 140/100) selected cDNAs in a range between 150-350 bp. cDNAs were then A-tailed using Exo- Klenow, followed by ligation of sequencing adapter oligos. Following bead purification, dUTP was cleaved from the second strand using AmpErase Uracil N-glycosylase, resulting in adaptor ligated single stranded cDNAs. PGCGROWTHCONDITIONS
Sequenced reads were trimmed, the mapped to the Escherichia coli K-12 MG1655 genome (U00096.2) using SOAP. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample PGCGROWTHCONDITIONS
Total RNA was extracted from cell pellets by hot phenol extraction. The integrity of total RNA was determined from agarose gel or microchannel electrophoretograms. 16S and 23S Ribosomal RNA was depleted prior to construction of RNAseq libraries using MICROBExpress reagents. PGCGROWTHCONDITIONS
Base calling was performed by the DOE Joint Genome Institute using Illumina software. PGCGROWTHCONDITIONS
Cells were grown in MOPS minimal medium with 0.2% glucose at 37 oC  in gas-sparged Roux bottles or shaking flasks to mid-log phase (OD600 ~ 0.3-0.4). PGCGROWTHCONDITIONS
Counts per million unique reads were calculated for each gene. PGCGROWTHCONDITIONS
Cultures were transferred directly into an ice-cold ethanol/phenol stop solution, which immediately inactivated cellular RNases. Cells were collected by centrifugation and stored at -80 oC until RNA extraction. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Genome_build: U00096.2 PGCGROWTHCONDITIONS
genotype/variation: wild-type PGCGROWTHCONDITIONS
MG1655 + 20 ug/ml bicyclomycin 2 PGCGROWTHCONDITIONS
MG1655 + 20 ug/ml bicyclomycin PGCGROWTHCONDITIONS
molecule subtype: ribosome-depeleted RNA PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-Seq was performed by the DOE Joint Genome Institute using the dUTP method. Briefly, ribosome-depleted RNA was fragmented in a buffered zinc solution, then purified using AMPure SPRI beads. First-strand cDNAs were then synthesized from the fragmented RNA using Superscript II reverse transcriptase, followed by a second bead purification. dUTP was included in the second strand synthesis reaction in addition to dTTP to chemically mark the second strand.  Two further bead purification steps using different ratios of beads to cDNA (85/100, then 140/100) selected cDNAs in a range between 150-350 bp. cDNAs were then A-tailed using Exo- Klenow, followed by ligation of sequencing adapter oligos. Following bead purification, dUTP was cleaved from the second strand using AmpErase Uracil N-glycosylase, resulting in adaptor ligated single stranded cDNAs. PGCGROWTHCONDITIONS
Sequenced reads were trimmed, the mapped to the Escherichia coli K-12 MG1655 genome (U00096.2) using SOAP. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample PGCGROWTHCONDITIONS
Total RNA was extracted from cell pellets by hot phenol extraction. The integrity of total RNA was determined from agarose gel or microchannel electrophoretograms. 16S and 23S Ribosomal RNA was depleted prior to construction of RNAseq libraries using MICROBExpress reagents. PGCGROWTHCONDITIONS
37C in LB medium under aerobic and anaerobic condition PGCGROWTHCONDITIONS
E.coli Top 10 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: GI:170079663/NC_010473 PGCGROWTHCONDITIONS
genotype/variation: no LL37 expression (control) PGCGROWTHCONDITIONS
growth condition: aerobic PGCGROWTHCONDITIONS
mRNA of prokaryotes is enriched just by removing rRNAs from the total RNA. Adding the fragmentation buffer, the mRNA is interrupted to short fragments (about 200 bp), then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to sythsize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. PGCGROWTHCONDITIONS
pHerd30T CK+aerobic PGCGROWTHCONDITIONS
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CLC Genomics Workbench, default parameters PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to DH10B gene using CLC Genomics Workbench, default parameters PGCGROWTHCONDITIONS
sequencing adaptors are ligated to the fragments. The required fragments is purified by agrose gel electrophoresis and enriched by PCR amplification. The library products are ready for sequencing analysis via Illumina HiSeq™ 2000. PGCGROWTHCONDITIONS
strain: E.coli Top 10 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample PGCGROWTHCONDITIONS
The original image data is transfered into sequence data by base calling PGCGROWTHCONDITIONS
Total RNA was isolated with TRIzol (invitrogen, Carlsbad, CA) according to the manufacture's instruction. DNA was removed from RNA extracts with RNase-free DNase I (New England Biolabs, Beverly, MA, USA) by incubation at 37°C for 30 min. The quality of total RNA was assessed by using 2100 Bioanalyzer (Agilent, Santa Clara, USA) and also checked by agarose gel electrophoresis. rRNAs was subsquently removed from the total mRNA following the instruction of the Ribo-Zero rRNATM Removal kit (Epicentre, Madison, WI, USA). PGCGROWTHCONDITIONS
37C in LB medium under aerobic and anaerobic condition PGCGROWTHCONDITIONS
E.coli Top 10 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: GI:170079663/NC_010473 PGCGROWTHCONDITIONS
genotype/variation: LL37 expression induced PGCGROWTHCONDITIONS
growth condition: aerobic PGCGROWTHCONDITIONS
mRNA of prokaryotes is enriched just by removing rRNAs from the total RNA. Adding the fragmentation buffer, the mRNA is interrupted to short fragments (about 200 bp), then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to sythsize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. PGCGROWTHCONDITIONS
pHerd30T-LL37 induced+aerobic PGCGROWTHCONDITIONS
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CLC Genomics Workbench, default parameters PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to DH10B gene using CLC Genomics Workbench, default parameters PGCGROWTHCONDITIONS
sequencing adaptors are ligated to the fragments. The required fragments is purified by agrose gel electrophoresis and enriched by PCR amplification. The library products are ready for sequencing analysis via Illumina HiSeq™ 2000. PGCGROWTHCONDITIONS
strain: E.coli Top 10 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample PGCGROWTHCONDITIONS
The original image data is transfered into sequence data by base calling PGCGROWTHCONDITIONS
Total RNA was isolated with TRIzol (invitrogen, Carlsbad, CA) according to the manufacture's instruction. DNA was removed from RNA extracts with RNase-free DNase I (New England Biolabs, Beverly, MA, USA) by incubation at 37°C for 30 min. The quality of total RNA was assessed by using 2100 Bioanalyzer (Agilent, Santa Clara, USA) and also checked by agarose gel electrophoresis. rRNAs was subsquently removed from the total mRNA following the instruction of the Ribo-Zero rRNATM Removal kit (Epicentre, Madison, WI, USA). PGCGROWTHCONDITIONS
37C in LB medium under aerobic and anaerobic condition PGCGROWTHCONDITIONS
E.coli Top 10 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: GI:170079663/NC_010473 PGCGROWTHCONDITIONS
genotype/variation: no LL37 expression (control) PGCGROWTHCONDITIONS
growth condition: anaerobic PGCGROWTHCONDITIONS
mRNA of prokaryotes is enriched just by removing rRNAs from the total RNA. Adding the fragmentation buffer, the mRNA is interrupted to short fragments (about 200 bp), then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to sythsize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. PGCGROWTHCONDITIONS
pHerd30T-LL37 CK+ anaerobic PGCGROWTHCONDITIONS
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CLC Genomics Workbench, default parameters PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to DH10B gene using CLC Genomics Workbench, default parameters PGCGROWTHCONDITIONS
sequencing adaptors are ligated to the fragments. The required fragments is purified by agrose gel electrophoresis and enriched by PCR amplification. The library products are ready for sequencing analysis via Illumina HiSeq™ 2000. PGCGROWTHCONDITIONS
strain: E.coli Top 10 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample PGCGROWTHCONDITIONS
The original image data is transfered into sequence data by base calling PGCGROWTHCONDITIONS
Total RNA was isolated with TRIzol (invitrogen, Carlsbad, CA) according to the manufacture's instruction. DNA was removed from RNA extracts with RNase-free DNase I (New England Biolabs, Beverly, MA, USA) by incubation at 37°C for 30 min. The quality of total RNA was assessed by using 2100 Bioanalyzer (Agilent, Santa Clara, USA) and also checked by agarose gel electrophoresis. rRNAs was subsquently removed from the total mRNA following the instruction of the Ribo-Zero rRNATM Removal kit (Epicentre, Madison, WI, USA). PGCGROWTHCONDITIONS
37C in LB medium under aerobic and anaerobic condition PGCGROWTHCONDITIONS
E.coli Top 10 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: GI:170079663/NC_010473 PGCGROWTHCONDITIONS
genotype/variation: LL37 expression induced PGCGROWTHCONDITIONS
growth condition: anaerobic PGCGROWTHCONDITIONS
mRNA of prokaryotes is enriched just by removing rRNAs from the total RNA. Adding the fragmentation buffer, the mRNA is interrupted to short fragments (about 200 bp), then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to sythsize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. PGCGROWTHCONDITIONS
pHerd30T-LL37 induced +anaerobic PGCGROWTHCONDITIONS
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CLC Genomics Workbench, default parameters PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to DH10B gene using CLC Genomics Workbench, default parameters PGCGROWTHCONDITIONS
sequencing adaptors are ligated to the fragments. The required fragments is purified by agrose gel electrophoresis and enriched by PCR amplification. The library products are ready for sequencing analysis via Illumina HiSeq™ 2000. PGCGROWTHCONDITIONS
strain: E.coli Top 10 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample PGCGROWTHCONDITIONS
The original image data is transfered into sequence data by base calling PGCGROWTHCONDITIONS
Total RNA was isolated with TRIzol (invitrogen, Carlsbad, CA) according to the manufacture's instruction. DNA was removed from RNA extracts with RNase-free DNase I (New England Biolabs, Beverly, MA, USA) by incubation at 37°C for 30 min. The quality of total RNA was assessed by using 2100 Bioanalyzer (Agilent, Santa Clara, USA) and also checked by agarose gel electrophoresis. rRNAs was subsquently removed from the total mRNA following the instruction of the Ribo-Zero rRNATM Removal kit (Epicentre, Madison, WI, USA). PGCGROWTHCONDITIONS
All RNA data were mapped to the reference genome Xuzhou21 using SOAP2. PGCGROWTHCONDITIONS
Escherichia coli O157:H7 PGCGROWTHCONDITIONS
For total RNA isolation, the bacteria were inoculated in 5 ml LB broth at 37℃with shaking for 16 h. 50 µl of the above culture was inoculated in 5 ml fresh LB broth and the culture was shaken at 37°C for about 2.5 h until the OD600 reached 0.6. 500 µl of the culture were mixed with 1 ml RNA protect bacterial reagent (Qiagen, Hilden, Germany) to stabilize RNA according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
Isolated from feces of a HUS patient from an outbreak in China in 1999 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: Xuzhou21 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample PGCGROWTHCONDITIONS
The bacteria were routinely grown in Luria-Bertani (LB) broth or on LB agar plates (pH 7.2). PGCGROWTHCONDITIONS
The distribution of reads was plotted by its location in the reference genome, and then divided into gene region and intergenic region. Genome and gene coverage was calculated by counting the number of reads mapped to the genome and individual genes respectively. PGCGROWTHCONDITIONS
The gene expression was calculated using the RPKM method PGCGROWTHCONDITIONS
The total RNA extracted from Xuzhou21 and Xuzhou21m were first treated with Ribo-Zero™ rRNA Removal kit to remove rRNA. The mRNA was fragmented and produced cDNA libraries primed with random hexamers. cDNA was selected by size, amplificated using PCR and and then sent to sequencing using Illumina HiseqTM 2000 commercially. PGCGROWTHCONDITIONS
Total RNA were then isolated according to the standard protocol using an RNeasy mini kit (Qiagen). Genomic DNA were extracted from both Xuzhou21 and Xuzhou21m using Wizard Genomic DNA purification kit (Promega, Madison, WI, USA) according to the manufacturer’s protocols. PGCGROWTHCONDITIONS
WT rep1 PGCGROWTHCONDITIONS
All RNA data were mapped to the reference genome Xuzhou21 using SOAP2. PGCGROWTHCONDITIONS
Escherichia coli O157:H7 PGCGROWTHCONDITIONS
For total RNA isolation, the bacteria were inoculated in 5 ml LB broth at 37℃with shaking for 16 h. 50 µl of the above culture was inoculated in 5 ml fresh LB broth and the culture was shaken at 37°C for about 2.5 h until the OD600 reached 0.6. 500 µl of the culture were mixed with 1 ml RNA protect bacterial reagent (Qiagen, Hilden, Germany) to stabilize RNA according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
Isolated from feces of a HUS patient from an outbreak in China in 1999 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: Xuzhou21 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample PGCGROWTHCONDITIONS
The bacteria were routinely grown in Luria-Bertani (LB) broth or on LB agar plates (pH 7.2). PGCGROWTHCONDITIONS
The distribution of reads was plotted by its location in the reference genome, and then divided into gene region and intergenic region. Genome and gene coverage was calculated by counting the number of reads mapped to the genome and individual genes respectively. PGCGROWTHCONDITIONS
The gene expression was calculated using the RPKM method PGCGROWTHCONDITIONS
The total RNA extracted from Xuzhou21 and Xuzhou21m were first treated with Ribo-Zero™ rRNA Removal kit to remove rRNA. The mRNA was fragmented and produced cDNA libraries primed with random hexamers. cDNA was selected by size, amplificated using PCR and and then sent to sequencing using Illumina HiseqTM 2000 commercially. PGCGROWTHCONDITIONS
Total RNA were then isolated according to the standard protocol using an RNeasy mini kit (Qiagen). Genomic DNA were extracted from both Xuzhou21 and Xuzhou21m using Wizard Genomic DNA purification kit (Promega, Madison, WI, USA) according to the manufacturer’s protocols. PGCGROWTHCONDITIONS
WT rep2 PGCGROWTHCONDITIONS
All RNA data were mapped to the reference genome Xuzhou21 using SOAP2. PGCGROWTHCONDITIONS
Escherichia coli O157:H7 PGCGROWTHCONDITIONS
For total RNA isolation, the bacteria were inoculated in 5 ml LB broth at 37℃with shaking for 16 h. 50 µl of the above culture was inoculated in 5 ml fresh LB broth and the culture was shaken at 37°C for about 2.5 h until the OD600 reached 0.6. 500 µl of the culture were mixed with 1 ml RNA protect bacterial reagent (Qiagen, Hilden, Germany) to stabilize RNA according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
genotype: plasmid cured strain PGCGROWTHCONDITIONS
plasmid cured rep1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: Xuzhou21m PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample PGCGROWTHCONDITIONS
The bacteria were routinely grown in Luria-Bertani (LB) broth or on LB agar plates (pH 7.2). PGCGROWTHCONDITIONS
The distribution of reads was plotted by its location in the reference genome, and then divided into gene region and intergenic region. Genome and gene coverage was calculated by counting the number of reads mapped to the genome and individual genes respectively. PGCGROWTHCONDITIONS
The gene expression was calculated using the RPKM method PGCGROWTHCONDITIONS
The total RNA extracted from Xuzhou21 and Xuzhou21m were first treated with Ribo-Zero™ rRNA Removal kit to remove rRNA. The mRNA was fragmented and produced cDNA libraries primed with random hexamers. cDNA was selected by size, amplificated using PCR and and then sent to sequencing using Illumina HiseqTM 2000 commercially. PGCGROWTHCONDITIONS
Total RNA were then isolated according to the standard protocol using an RNeasy mini kit (Qiagen). Genomic DNA were extracted from both Xuzhou21 and Xuzhou21m using Wizard Genomic DNA purification kit (Promega, Madison, WI, USA) according to the manufacturer’s protocols. PGCGROWTHCONDITIONS
Xuzhou21 cured of the pO157_Sal plasmid PGCGROWTHCONDITIONS
All RNA data were mapped to the reference genome Xuzhou21 using SOAP2. PGCGROWTHCONDITIONS
Escherichia coli O157:H7 PGCGROWTHCONDITIONS
For total RNA isolation, the bacteria were inoculated in 5 ml LB broth at 37℃with shaking for 16 h. 50 µl of the above culture was inoculated in 5 ml fresh LB broth and the culture was shaken at 37°C for about 2.5 h until the OD600 reached 0.6. 500 µl of the culture were mixed with 1 ml RNA protect bacterial reagent (Qiagen, Hilden, Germany) to stabilize RNA according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
genotype: plasmid cured strain PGCGROWTHCONDITIONS
plasmid cured rep2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: Xuzhou21m PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample PGCGROWTHCONDITIONS
The bacteria were routinely grown in Luria-Bertani (LB) broth or on LB agar plates (pH 7.2). PGCGROWTHCONDITIONS
The distribution of reads was plotted by its location in the reference genome, and then divided into gene region and intergenic region. Genome and gene coverage was calculated by counting the number of reads mapped to the genome and individual genes respectively. PGCGROWTHCONDITIONS
The gene expression was calculated using the RPKM method PGCGROWTHCONDITIONS
The total RNA extracted from Xuzhou21 and Xuzhou21m were first treated with Ribo-Zero™ rRNA Removal kit to remove rRNA. The mRNA was fragmented and produced cDNA libraries primed with random hexamers. cDNA was selected by size, amplificated using PCR and and then sent to sequencing using Illumina HiseqTM 2000 commercially. PGCGROWTHCONDITIONS
Total RNA were then isolated according to the standard protocol using an RNeasy mini kit (Qiagen). Genomic DNA were extracted from both Xuzhou21 and Xuzhou21m using Wizard Genomic DNA purification kit (Promega, Madison, WI, USA) according to the manufacturer’s protocols. PGCGROWTHCONDITIONS
Xuzhou21 cured of the pO157_Sal plasmid PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
BL21_1 PGCGROWTHCONDITIONS
Cells were grown in a 250 ml fermenter containing 100 ml LB medium supplemented  with 3 g/L glucose, 0.1 mM IPTG, and 50 μg/mL antibiotics. The fermentors were operated at 37 °C and 250 rpm with  aeration (200 mL/min). Flow rate was 1.162ml/min(dilution rate 0,7/h). The pellets were used for RNA. PGCGROWTHCONDITIONS
condition: LB+3g/L Glc +0.1mM IPTG PGCGROWTHCONDITIONS
Escherichia coli BL21(DE3) PGCGROWTHCONDITIONS
First and second strand cDNA synthesis was carried out using the Ovation® Prokaryotic RNA-Seq System (NuGEN Technologies Inc., San Carlos, CA, USA), and NuGEN’s Encore NGS Library System was applied to construct the cDNA library for the IlluminaHiSeq platform. PGCGROWTHCONDITIONS
Genome_build: gi|387825439 PGCGROWTHCONDITIONS
genotype: wild-type PGCGROWTHCONDITIONS
Raw sequencing reads (FASTQ)were processed by Xpression and only the uniquely mapped reads were subjected to further analysis. PGCGROWTHCONDITIONS
Reference files for the genome sequence being queried, Escherichia coli BL21(DE3) genome (NC_012971) were uploaded. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: BL21(DE3) PGCGROWTHCONDITIONS
The number of reads overlapping each gene was recorded and normalized based on reads per kilobase per million (RPKM) uniquely mapped reads. PGCGROWTHCONDITIONS
Total RNA was harvested from C. glutamicum cells using TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) and NucleoSpin® (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions with the following modifications. Cells were harvested by centrifugation, resuspended in TRIzol® reagent, and transferred to a vial containing Lysing Matrix B® (MP Biomedicals, Solon, OH, USA) for lysis. The suspension was centrifuged, and the supernatant was applied to a NucleoSpin® RNA II kit for purification. PGCGROWTHCONDITIONS
Xpression (https://depts.washington.edu/cshlab/html/rnaseq.html) was used for RNA-Seq data processing. PGCGROWTHCONDITIONS
Xpression was used for filtering and trimming reads. PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
BL21_2 PGCGROWTHCONDITIONS
Cells were grown in a 250 ml fermenter containing 100 ml LB medium supplemented  with 3 g/L glucose, 0.1 mM IPTG, and 50 μg/mL antibiotics. The fermentors were operated at 37 °C and 250 rpm with  aeration (200 mL/min). Flow rate was 1.162ml/min(dilution rate 0,7/h). The pellets were used for RNA. PGCGROWTHCONDITIONS
condition: LB+3g/L Glc +0.1mM IPTG PGCGROWTHCONDITIONS
Escherichia coli BL21(DE3) PGCGROWTHCONDITIONS
First and second strand cDNA synthesis was carried out using the Ovation® Prokaryotic RNA-Seq System (NuGEN Technologies Inc., San Carlos, CA, USA), and NuGEN’s Encore NGS Library System was applied to construct the cDNA library for the IlluminaHiSeq platform. PGCGROWTHCONDITIONS
Genome_build: gi|387825439 PGCGROWTHCONDITIONS
genotype: wild-type PGCGROWTHCONDITIONS
Raw sequencing reads (FASTQ)were processed by Xpression and only the uniquely mapped reads were subjected to further analysis. PGCGROWTHCONDITIONS
Reference files for the genome sequence being queried, Escherichia coli BL21(DE3) genome (NC_012971) were uploaded. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: BL21(DE3) PGCGROWTHCONDITIONS
The number of reads overlapping each gene was recorded and normalized based on reads per kilobase per million (RPKM) uniquely mapped reads. PGCGROWTHCONDITIONS
Total RNA was harvested from C. glutamicum cells using TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) and NucleoSpin® (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions with the following modifications. Cells were harvested by centrifugation, resuspended in TRIzol® reagent, and transferred to a vial containing Lysing Matrix B® (MP Biomedicals, Solon, OH, USA) for lysis. The suspension was centrifuged, and the supernatant was applied to a NucleoSpin® RNA II kit for purification. PGCGROWTHCONDITIONS
Xpression (https://depts.washington.edu/cshlab/html/rnaseq.html) was used for RNA-Seq data processing. PGCGROWTHCONDITIONS
Xpression was used for filtering and trimming reads. PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
Cells were grown in a 250 ml fermenter containing 100 ml LB medium supplemented  with 3 g/L glucose, 0.1 mM IPTG, and 50 μg/mL antibiotics. The fermentors were operated at 37 °C and 250 rpm with  aeration (200 mL/min). Flow rate was 1.162ml/min(dilution rate 0,7/h). The pellets were used for RNA. PGCGROWTHCONDITIONS
condition: LB+3g/L Glc +0.1mM IPTG + 50μg/ml Amp PGCGROWTHCONDITIONS
Escherichia coli BL21(DE3) PGCGROWTHCONDITIONS
First and second strand cDNA synthesis was carried out using the Ovation® Prokaryotic RNA-Seq System (NuGEN Technologies Inc., San Carlos, CA, USA), and NuGEN’s Encore NGS Library System was applied to construct the cDNA library for the IlluminaHiSeq platform. PGCGROWTHCONDITIONS
Genome_build: gi|387825439 PGCGROWTHCONDITIONS
genotype: Pck over-expressed PGCGROWTHCONDITIONS
PCK over PGCGROWTHCONDITIONS
Raw sequencing reads (FASTQ)were processed by Xpression and only the uniquely mapped reads were subjected to further analysis. PGCGROWTHCONDITIONS
Reference files for the genome sequence being queried, Escherichia coli BL21(DE3) genome (NC_012971) were uploaded. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: BL21(DE3) PGCGROWTHCONDITIONS
The number of reads overlapping each gene was recorded and normalized based on reads per kilobase per million (RPKM) uniquely mapped reads. PGCGROWTHCONDITIONS
Total RNA was harvested from C. glutamicum cells using TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) and NucleoSpin® (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions with the following modifications. Cells were harvested by centrifugation, resuspended in TRIzol® reagent, and transferred to a vial containing Lysing Matrix B® (MP Biomedicals, Solon, OH, USA) for lysis. The suspension was centrifuged, and the supernatant was applied to a NucleoSpin® RNA II kit for purification. PGCGROWTHCONDITIONS
Xpression (https://depts.washington.edu/cshlab/html/rnaseq.html) was used for RNA-Seq data processing. PGCGROWTHCONDITIONS
Xpression was used for filtering and trimming reads. PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Galaxy1-[CV104_pHDB3_5.txt] PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: Galaxy1-[CV104_pHDB3_5] PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich + 0.2% Glucose PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Galaxy6-[CV104_pHDB3_10.txt] PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: Galaxy6-[CV104_pHDB3_10] PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich + 0.2% Glucose PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Galaxy4-[CV104_pHDB3_20.txt] PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: Galaxy4-[CV104_pHDB3_20] PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich + 0.2% Glucose PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Galaxy2-[CV104_pLCV1_5.txt] PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: Galaxy2-[CV104_pLCV1_5] PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich + 0.2% Glucose PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Galaxy3-[CV104_pLCV1_10.txt] PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: Galaxy3-[CV104_pLCV1_10] PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich + 0.2% Glucose PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Galaxy5-[CV104_pLCV1_20.txt] PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: Galaxy5-[CV104_pLCV1_20] PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich + 0.2% Glucose PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: pHDB3 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich + 0.2% Glucose PGCGROWTHCONDITIONS
pHDB3_1 PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: pHDB3 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich + 0.2% Glucose PGCGROWTHCONDITIONS
pHDB3_2 PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: pHDB3 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich + 0.2% Glucose PGCGROWTHCONDITIONS
pHDB3_3 PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: pLCV1 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich + 0.2% Glucose PGCGROWTHCONDITIONS
pLCV1_1 PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: pLCV1 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich + 0.2% Glucose PGCGROWTHCONDITIONS
pLCV1_2 PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: pLCV1 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich + 0.2% Glucose PGCGROWTHCONDITIONS
pLCV1_3 PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: MG1655 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
MG1655-aMG_1 PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: MG1655 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
MG1655-aMG_2 PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: MG1655 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
MG1655-aMG_3 PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: MG1655 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: LB + 0.5% aMG PGCGROWTHCONDITIONS
MG1655+aMG_1 PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: MG1655 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: LB + 0.5% aMG PGCGROWTHCONDITIONS
MG1655+aMG_2 PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: MG1655 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: LB + 0.5% aMG PGCGROWTHCONDITIONS
MG1655+aMG_3 PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: SgrR PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: LB + 0.5% aMG PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
SgrR_1 PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: SgrR PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: LB + 0.5% aMG PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
SgrR_2 PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: SgrR PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: LB + 0.5% aMG PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
SgrR_3 PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: sgrS PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich + 0.4% Glycerol +0.5% aMG PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
sgrS_T_1 PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: sgrS PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich + 0.4% Glycerol +0.5% aMG PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
sgrS_T_2 PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: sgrS PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich + 0.4% Glycerol +0.5% aMG PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
sgrS_T_3 PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: sgrS PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich+ 0.4% Glycerol PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
sgrS_un_1 PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: sgrS PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich+ 0.4% Glycerol PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
sgrS_un_2 PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: sgrS PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich+ 0.4% Glycerol PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
sgrS_un_3 PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: WT PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: LB + 0.5% aMG PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
WT_1 PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: WT PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: LB + 0.5% aMG PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
WT_2 PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: WT PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: LB + 0.5% aMG PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
WT_3 PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: WT PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich + 0.4% Glycerol +0.5% aMG PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
wt_T_1 PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: WT PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich + 0.4% Glycerol +0.5% aMG PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
wt_T_2 PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: WT PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich + 0.4% Glycerol +0.5% aMG PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
wt_T_3 PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: WT PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich+ 0.4% Glycerol PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
wt_un_1 PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: WT PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich+ 0.4% Glycerol PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
wt_un_2 PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: WT PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Rich+ 0.4% Glycerol PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
wt_un_3 PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
CV108_minus_aMG_1 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: CV108 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Minimal + 0.4% Glycerol PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
CV108_minus_aMG_2 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: CV108 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Minimal + 0.4% Glycerol PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
CV108_minus_aMG_3 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: CV108 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Minimal + 0.4% Glycerol PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
CV108_plus_aMG_1 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: CV108 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Minimal + 0.4% Glycerol +0.5% aMG PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
CV108_plus_aMG_2 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: CV108 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Minimal + 0.4% Glycerol +0.5% aMG PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
CV108_plus_aMG_3 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: CV108 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Minimal + 0.4% Glycerol +0.5% aMG PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: MG1655 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Minimal + 0.4% Glycerol PGCGROWTHCONDITIONS
MG1655_minus_aMG_1 PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: MG1655 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Minimal + 0.4% Glycerol PGCGROWTHCONDITIONS
MG1655_minus_aMG_2 PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: MG1655 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Minimal + 0.4% Glycerol PGCGROWTHCONDITIONS
MG1655_minus_aMG_3 PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: MG1655 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Minimal + 0.4% Glycerol +0.5% aMG PGCGROWTHCONDITIONS
MG1655_plus_aMG_1 PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: MG1655 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Minimal + 0.4% Glycerol +0.5% aMG PGCGROWTHCONDITIONS
MG1655_plus_aMG_2 PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: MG1655 PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Minimal + 0.4% Glycerol +0.5% aMG PGCGROWTHCONDITIONS
MG1655_plus_aMG_3 PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: WT PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Minimal + 0.4% Glycerol PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
WT_minus_2DG_1 PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: WT PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Minimal + 0.4% Glycerol PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
WT_minus_2DG_2 PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: WT PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Minimal + 0.4% Glycerol PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
WT_minus_2DG_3 PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: WT PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Minimal + 0.4% Glycerol +0.5% 2-DG PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
WT_plus_2DG_1 PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: WT PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Minimal + 0.4% Glycerol +0.5% 2-DG PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
WT_plus_2DG_2 PGCGROWTHCONDITIONS
Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS
Cells treated during mid-exponential growth phase PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 substr. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: WT PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. PGCGROWTHCONDITIONS
media: Defined MOPS Minimal + 0.4% Glycerol +0.5% 2-DG PGCGROWTHCONDITIONS
Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into  indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates. PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
WT_plus_2DG_3 PGCGROWTHCONDITIONS
Among potential TSSs, only TSSs with the strongest signal within 10 bp window were kept to remove possible noise signals, and TSSs with greater than or equal to 40% of the strongest signal upstream of an annotated gene were considered as multiple TSSs. PGCGROWTHCONDITIONS
Cells at stationary phase (OD600nm 1.5) in M9 glucose media PGCGROWTHCONDITIONS
E. coli K12 MG1655 was grown to mid-log phase (O.D.600nm 0.5) or to stationary phase (O.D.600nm 1.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose or W2 minimal media supplemented with 0.2% glucose and 0.2% glutamine. For heatshock conditions, cells were grown to mid-log phase and incubated at 42oC for 10 min. PGCGROWTHCONDITIONS
E. coli stationary 1 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913/ASM584v1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequence reads for cDNA libraries were aligned onto E. coli K12 MG1655 genome, using Mosaik with following arguments: hash size=10, mismatch=0. Only reads that aligned to the unique genomic location were retained. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: counts PGCGROWTHCONDITIONS
The amplified cDNA libraries from two biological replicates for each E. coli were sequenced on an Illumina Genome Analyzer. Sequence reads for cDNA libraries were aligned onto E. coli K12 MG1655 genome, using Mosaik with following arguments: hash size=10, mismatch=0. Only reads that aligned to the unique genomic location were retained. Two biological replicates were processed seperatedly, and only sequence reads presented in both biological replciates were considered for further process. The genomic coordinates of the 5'-end of these uniquely aligned reads were defined as potential TSSs. Among potential TSSs, only TSSs with the strongest signal within 10 bp window were kept to remove possible noise signals, and TSSs with greater than or equal to 40% of the strongest signal upstream of an annotated gene were considered as multiple TSSs. PGCGROWTHCONDITIONS
The cell culture was treated with the RNAprotect reagent (Qiagen). PGCGROWTHCONDITIONS
Total mRNA isolated from each cell culture was treated with Terminator 5' Phosphate Dependent Exonuclease (Epicentre) to enrich 5' tri-phosphorylated mRNAs. Intact tri-phosphorylated RNAs were then treated with RNA 5'-Polyphosphatase (Epicentre) to generate 5'-end monophosphorylated RNA for ligation to RNA adaptors. cDNAs were synthesized using the adaptor-ligated mRNAs as template using a modified small RNA RT primer from Illumina and Superscript II Reverse Transcriptase (Invitrogen). The cDNA samples were amplified, and size fractionated from 100 to 300 bp. PGCGROWTHCONDITIONS
treatment: stationary phase PGCGROWTHCONDITIONS
Two biological replicates were processed seperatedly, and only sequence reads presented in both biological replciates were considered for further process. The genomic coordinates of the 5'-end of these uniquely aligned reads were defined as potential TSSs. PGCGROWTHCONDITIONS
Among potential TSSs, only TSSs with the strongest signal within 10 bp window were kept to remove possible noise signals, and TSSs with greater than or equal to 40% of the strongest signal upstream of an annotated gene were considered as multiple TSSs. PGCGROWTHCONDITIONS
Cells at stationary phase (OD600nm 1.5) in M9 glucose media PGCGROWTHCONDITIONS
E. coli K12 MG1655 was grown to mid-log phase (O.D.600nm 0.5) or to stationary phase (O.D.600nm 1.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose or W2 minimal media supplemented with 0.2% glucose and 0.2% glutamine. For heatshock conditions, cells were grown to mid-log phase and incubated at 42oC for 10 min. PGCGROWTHCONDITIONS
E. coli stationary 2 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913/ASM584v1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequence reads for cDNA libraries were aligned onto E. coli K12 MG1655 genome, using Mosaik with following arguments: hash size=10, mismatch=0. Only reads that aligned to the unique genomic location were retained. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: counts PGCGROWTHCONDITIONS
The amplified cDNA libraries from two biological replicates for each E. coli were sequenced on an Illumina Genome Analyzer. Sequence reads for cDNA libraries were aligned onto E. coli K12 MG1655 genome, using Mosaik with following arguments: hash size=10, mismatch=0. Only reads that aligned to the unique genomic location were retained. Two biological replicates were processed seperatedly, and only sequence reads presented in both biological replciates were considered for further process. The genomic coordinates of the 5'-end of these uniquely aligned reads were defined as potential TSSs. Among potential TSSs, only TSSs with the strongest signal within 10 bp window were kept to remove possible noise signals, and TSSs with greater than or equal to 40% of the strongest signal upstream of an annotated gene were considered as multiple TSSs. PGCGROWTHCONDITIONS
The cell culture was treated with the RNAprotect reagent (Qiagen). PGCGROWTHCONDITIONS
Total mRNA isolated from each cell culture was treated with Terminator 5' Phosphate Dependent Exonuclease (Epicentre) to enrich 5' tri-phosphorylated mRNAs. Intact tri-phosphorylated RNAs were then treated with RNA 5'-Polyphosphatase (Epicentre) to generate 5'-end monophosphorylated RNA for ligation to RNA adaptors. cDNAs were synthesized using the adaptor-ligated mRNAs as template using a modified small RNA RT primer from Illumina and Superscript II Reverse Transcriptase (Invitrogen). The cDNA samples were amplified, and size fractionated from 100 to 300 bp. PGCGROWTHCONDITIONS
treatment: stationary phase PGCGROWTHCONDITIONS
Two biological replicates were processed seperatedly, and only sequence reads presented in both biological replciates were considered for further process. The genomic coordinates of the 5'-end of these uniquely aligned reads were defined as potential TSSs. PGCGROWTHCONDITIONS
Among potential TSSs, only TSSs with the strongest signal within 10 bp window were kept to remove possible noise signals, and TSSs with greater than or equal to 40% of the strongest signal upstream of an annotated gene were considered as multiple TSSs. PGCGROWTHCONDITIONS
Cells at mid-log phase (OD600nm 0.5) in W2 media supplemented with 0.2% glucose and 0.2% glutamine PGCGROWTHCONDITIONS
E. coli glutamine 1 PGCGROWTHCONDITIONS
E. coli K12 MG1655 was grown to mid-log phase (O.D.600nm 0.5) or to stationary phase (O.D.600nm 1.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose or W2 minimal media supplemented with 0.2% glucose and 0.2% glutamine. For heatshock conditions, cells were grown to mid-log phase and incubated at 42oC for 10 min. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913/ASM584v1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequence reads for cDNA libraries were aligned onto E. coli K12 MG1655 genome, using Mosaik with following arguments: hash size=10, mismatch=0. Only reads that aligned to the unique genomic location were retained. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: counts PGCGROWTHCONDITIONS
The amplified cDNA libraries from two biological replicates for each E. coli were sequenced on an Illumina Genome Analyzer. Sequence reads for cDNA libraries were aligned onto E. coli K12 MG1655 genome, using Mosaik with following arguments: hash size=10, mismatch=0. Only reads that aligned to the unique genomic location were retained. Two biological replicates were processed seperatedly, and only sequence reads presented in both biological replciates were considered for further process. The genomic coordinates of the 5'-end of these uniquely aligned reads were defined as potential TSSs. Among potential TSSs, only TSSs with the strongest signal within 10 bp window were kept to remove possible noise signals, and TSSs with greater than or equal to 40% of the strongest signal upstream of an annotated gene were considered as multiple TSSs. PGCGROWTHCONDITIONS
The cell culture was treated with the RNAprotect reagent (Qiagen). PGCGROWTHCONDITIONS
Total mRNA isolated from each cell culture was treated with Terminator 5' Phosphate Dependent Exonuclease (Epicentre) to enrich 5' tri-phosphorylated mRNAs. Intact tri-phosphorylated RNAs were then treated with RNA 5'-Polyphosphatase (Epicentre) to generate 5'-end monophosphorylated RNA for ligation to RNA adaptors. cDNAs were synthesized using the adaptor-ligated mRNAs as template using a modified small RNA RT primer from Illumina and Superscript II Reverse Transcriptase (Invitrogen). The cDNA samples were amplified, and size fractionated from 100 to 300 bp. PGCGROWTHCONDITIONS
treatment: glutamine PGCGROWTHCONDITIONS
Two biological replicates were processed seperatedly, and only sequence reads presented in both biological replciates were considered for further process. The genomic coordinates of the 5'-end of these uniquely aligned reads were defined as potential TSSs. PGCGROWTHCONDITIONS
Among potential TSSs, only TSSs with the strongest signal within 10 bp window were kept to remove possible noise signals, and TSSs with greater than or equal to 40% of the strongest signal upstream of an annotated gene were considered as multiple TSSs. PGCGROWTHCONDITIONS
Cells at mid-log phase (OD600nm 0.5) in W2 media supplemented with 0.2% glucose and 0.2% glutamine PGCGROWTHCONDITIONS
E. coli glutamine 2 PGCGROWTHCONDITIONS
E. coli K12 MG1655 was grown to mid-log phase (O.D.600nm 0.5) or to stationary phase (O.D.600nm 1.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose or W2 minimal media supplemented with 0.2% glucose and 0.2% glutamine. For heatshock conditions, cells were grown to mid-log phase and incubated at 42oC for 10 min. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913/ASM584v1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequence reads for cDNA libraries were aligned onto E. coli K12 MG1655 genome, using Mosaik with following arguments: hash size=10, mismatch=0. Only reads that aligned to the unique genomic location were retained. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: counts PGCGROWTHCONDITIONS
The amplified cDNA libraries from two biological replicates for each E. coli were sequenced on an Illumina Genome Analyzer. Sequence reads for cDNA libraries were aligned onto E. coli K12 MG1655 genome, using Mosaik with following arguments: hash size=10, mismatch=0. Only reads that aligned to the unique genomic location were retained. Two biological replicates were processed seperatedly, and only sequence reads presented in both biological replciates were considered for further process. The genomic coordinates of the 5'-end of these uniquely aligned reads were defined as potential TSSs. Among potential TSSs, only TSSs with the strongest signal within 10 bp window were kept to remove possible noise signals, and TSSs with greater than or equal to 40% of the strongest signal upstream of an annotated gene were considered as multiple TSSs. PGCGROWTHCONDITIONS
The cell culture was treated with the RNAprotect reagent (Qiagen). PGCGROWTHCONDITIONS
Total mRNA isolated from each cell culture was treated with Terminator 5' Phosphate Dependent Exonuclease (Epicentre) to enrich 5' tri-phosphorylated mRNAs. Intact tri-phosphorylated RNAs were then treated with RNA 5'-Polyphosphatase (Epicentre) to generate 5'-end monophosphorylated RNA for ligation to RNA adaptors. cDNAs were synthesized using the adaptor-ligated mRNAs as template using a modified small RNA RT primer from Illumina and Superscript II Reverse Transcriptase (Invitrogen). The cDNA samples were amplified, and size fractionated from 100 to 300 bp. PGCGROWTHCONDITIONS
treatment: glutamine PGCGROWTHCONDITIONS
Two biological replicates were processed seperatedly, and only sequence reads presented in both biological replciates were considered for further process. The genomic coordinates of the 5'-end of these uniquely aligned reads were defined as potential TSSs. PGCGROWTHCONDITIONS
Among potential TSSs, only TSSs with the strongest signal within 10 bp window were kept to remove possible noise signals, and TSSs with greater than or equal to 40% of the strongest signal upstream of an annotated gene were considered as multiple TSSs. PGCGROWTHCONDITIONS
Cells at mid-log phase (OD600nm 0.5) in M9 glucose (0.2%) media, with 42oC heatshock for 10 min. PGCGROWTHCONDITIONS
E. coli heatshock 1 PGCGROWTHCONDITIONS
E. coli K12 MG1655 was grown to mid-log phase (O.D.600nm 0.5) or to stationary phase (O.D.600nm 1.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose or W2 minimal media supplemented with 0.2% glucose and 0.2% glutamine. For heatshock conditions, cells were grown to mid-log phase and incubated at 42oC for 10 min. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913/ASM584v1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequence reads for cDNA libraries were aligned onto E. coli K12 MG1655 genome, using Mosaik with following arguments: hash size=10, mismatch=0. Only reads that aligned to the unique genomic location were retained. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: counts PGCGROWTHCONDITIONS
The amplified cDNA libraries from two biological replicates for each E. coli were sequenced on an Illumina Genome Analyzer. Sequence reads for cDNA libraries were aligned onto E. coli K12 MG1655 genome, using Mosaik with following arguments: hash size=10, mismatch=0. Only reads that aligned to the unique genomic location were retained. Two biological replicates were processed seperatedly, and only sequence reads presented in both biological replciates were considered for further process. The genomic coordinates of the 5'-end of these uniquely aligned reads were defined as potential TSSs. Among potential TSSs, only TSSs with the strongest signal within 10 bp window were kept to remove possible noise signals, and TSSs with greater than or equal to 40% of the strongest signal upstream of an annotated gene were considered as multiple TSSs. PGCGROWTHCONDITIONS
The cell culture was treated with the RNAprotect reagent (Qiagen). PGCGROWTHCONDITIONS
Total mRNA isolated from each cell culture was treated with Terminator 5' Phosphate Dependent Exonuclease (Epicentre) to enrich 5' tri-phosphorylated mRNAs. Intact tri-phosphorylated RNAs were then treated with RNA 5'-Polyphosphatase (Epicentre) to generate 5'-end monophosphorylated RNA for ligation to RNA adaptors. cDNAs were synthesized using the adaptor-ligated mRNAs as template using a modified small RNA RT primer from Illumina and Superscript II Reverse Transcriptase (Invitrogen). The cDNA samples were amplified, and size fractionated from 100 to 300 bp. PGCGROWTHCONDITIONS
treatment: heat shock PGCGROWTHCONDITIONS
Two biological replicates were processed seperatedly, and only sequence reads presented in both biological replciates were considered for further process. The genomic coordinates of the 5'-end of these uniquely aligned reads were defined as potential TSSs. PGCGROWTHCONDITIONS
Among potential TSSs, only TSSs with the strongest signal within 10 bp window were kept to remove possible noise signals, and TSSs with greater than or equal to 40% of the strongest signal upstream of an annotated gene were considered as multiple TSSs. PGCGROWTHCONDITIONS
Cells at mid-log phase (OD600nm 0.5) in M9 glucose (0.2%) media, with 42oC heatshock for 10 min. PGCGROWTHCONDITIONS
E. coli heatshock 2 PGCGROWTHCONDITIONS
E. coli K12 MG1655 was grown to mid-log phase (O.D.600nm 0.5) or to stationary phase (O.D.600nm 1.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose or W2 minimal media supplemented with 0.2% glucose and 0.2% glutamine. For heatshock conditions, cells were grown to mid-log phase and incubated at 42oC for 10 min. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913/ASM584v1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequence reads for cDNA libraries were aligned onto E. coli K12 MG1655 genome, using Mosaik with following arguments: hash size=10, mismatch=0. Only reads that aligned to the unique genomic location were retained. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: counts PGCGROWTHCONDITIONS
The amplified cDNA libraries from two biological replicates for each E. coli were sequenced on an Illumina Genome Analyzer. Sequence reads for cDNA libraries were aligned onto E. coli K12 MG1655 genome, using Mosaik with following arguments: hash size=10, mismatch=0. Only reads that aligned to the unique genomic location were retained. Two biological replicates were processed seperatedly, and only sequence reads presented in both biological replciates were considered for further process. The genomic coordinates of the 5'-end of these uniquely aligned reads were defined as potential TSSs. Among potential TSSs, only TSSs with the strongest signal within 10 bp window were kept to remove possible noise signals, and TSSs with greater than or equal to 40% of the strongest signal upstream of an annotated gene were considered as multiple TSSs. PGCGROWTHCONDITIONS
The cell culture was treated with the RNAprotect reagent (Qiagen). PGCGROWTHCONDITIONS
Total mRNA isolated from each cell culture was treated with Terminator 5' Phosphate Dependent Exonuclease (Epicentre) to enrich 5' tri-phosphorylated mRNAs. Intact tri-phosphorylated RNAs were then treated with RNA 5'-Polyphosphatase (Epicentre) to generate 5'-end monophosphorylated RNA for ligation to RNA adaptors. cDNAs were synthesized using the adaptor-ligated mRNAs as template using a modified small RNA RT primer from Illumina and Superscript II Reverse Transcriptase (Invitrogen). The cDNA samples were amplified, and size fractionated from 100 to 300 bp. PGCGROWTHCONDITIONS
treatment: heat shock PGCGROWTHCONDITIONS
Two biological replicates were processed seperatedly, and only sequence reads presented in both biological replciates were considered for further process. The genomic coordinates of the 5'-end of these uniquely aligned reads were defined as potential TSSs. PGCGROWTHCONDITIONS
culture/growth condition: LB (OD=0.87) PGCGROWTHCONDITIONS
E. coli cells_LB(OD=0.87) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For the Illumina GAII platform, the directional RNA-seq libraries were constructed by following an Illumina’s instruction using their Small RNA Sample Prep Kit with some modifications. For the HiSeq 2000 platform, the directional RNA-seq libraries were constructed using Illumina’s TruSeq Small RNA Sample Prep Kit. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K12 str MG1655 PGCGROWTHCONDITIONS
LB(OD=0.87) PGCGROWTHCONDITIONS
Merge the replicates for each sample. For example, for sample HS15min, merge HS15min_r1.HiSeq.fastq.gz, HS15min_r2.HiSeq.fastq.gz and HS15min_r3.HiSeq.fastq.gz to one fastq file PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, then mapped to E. coli K12 genome using bowtie v0.12.7 with parameters bowtie -t -v 3 -m 1 --best -S -p 2 PGCGROWTHCONDITIONS
strain: K12 PGCGROWTHCONDITIONS
substrain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWig files for whole-genome reads coverage (including number of mapped reads) for each sample. Each sample has two files, one for plus strand, and the other for minus strand. Therefore, there are 14 BigWig files for 7 samples. PGCGROWTHCONDITIONS
To enrich mRNAs and other transcripts, majority of rRNAs were removed from the DNase-treated total RNA using a MICROBExpress kit (Ambion) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Total RNA was isolated using a RiboPureTM -Bacteria Kit (Ambion) following the manufacturer’s instructions. Once isolated, ~10μg total RNA was treated with 8 units DNase (Invitrogen) twice to remove genomic DNA. PGCGROWTHCONDITIONS
Transform the mapped file format from sam to sorted bam which are later tranfered to bigWig, and separated by the strand (plus and minus). PGCGROWTHCONDITIONS
culture/growth condition: Heatshock 15min PGCGROWTHCONDITIONS
E. coli cells_HS15min PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For the Illumina GAII platform, the directional RNA-seq libraries were constructed by following an Illumina’s instruction using their Small RNA Sample Prep Kit with some modifications. For the HiSeq 2000 platform, the directional RNA-seq libraries were constructed using Illumina’s TruSeq Small RNA Sample Prep Kit. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K12 str MG1655 PGCGROWTHCONDITIONS
HS15min_r1_HiSeq PGCGROWTHCONDITIONS
Merge the replicates for each sample. For example, for sample HS15min, merge HS15min_r1.HiSeq.fastq.gz, HS15min_r2.HiSeq.fastq.gz and HS15min_r3.HiSeq.fastq.gz to one fastq file PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, then mapped to E. coli K12 genome using bowtie v0.12.7 with parameters bowtie -t -v 3 -m 1 --best -S -p 2 PGCGROWTHCONDITIONS
strain: K12 PGCGROWTHCONDITIONS
substrain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWig files for whole-genome reads coverage (including number of mapped reads) for each sample. Each sample has two files, one for plus strand, and the other for minus strand. Therefore, there are 14 BigWig files for 7 samples. PGCGROWTHCONDITIONS
To enrich mRNAs and other transcripts, majority of rRNAs were removed from the DNase-treated total RNA using a MICROBExpress kit (Ambion) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Total RNA was isolated using a RiboPureTM -Bacteria Kit (Ambion) following the manufacturer’s instructions. Once isolated, ~10μg total RNA was treated with 8 units DNase (Invitrogen) twice to remove genomic DNA. PGCGROWTHCONDITIONS
Transform the mapped file format from sam to sorted bam which are later tranfered to bigWig, and separated by the strand (plus and minus). PGCGROWTHCONDITIONS
culture/growth condition: Heatshock 15min PGCGROWTHCONDITIONS
E. coli cells_HS15min PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For the Illumina GAII platform, the directional RNA-seq libraries were constructed by following an Illumina’s instruction using their Small RNA Sample Prep Kit with some modifications. For the HiSeq 2000 platform, the directional RNA-seq libraries were constructed using Illumina’s TruSeq Small RNA Sample Prep Kit. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K12 str MG1655 PGCGROWTHCONDITIONS
HS15min_r2_HiSeq PGCGROWTHCONDITIONS
Merge the replicates for each sample. For example, for sample HS15min, merge HS15min_r1.HiSeq.fastq.gz, HS15min_r2.HiSeq.fastq.gz and HS15min_r3.HiSeq.fastq.gz to one fastq file PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, then mapped to E. coli K12 genome using bowtie v0.12.7 with parameters bowtie -t -v 3 -m 1 --best -S -p 2 PGCGROWTHCONDITIONS
strain: K12 PGCGROWTHCONDITIONS
substrain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWig files for whole-genome reads coverage (including number of mapped reads) for each sample. Each sample has two files, one for plus strand, and the other for minus strand. Therefore, there are 14 BigWig files for 7 samples. PGCGROWTHCONDITIONS
To enrich mRNAs and other transcripts, majority of rRNAs were removed from the DNase-treated total RNA using a MICROBExpress kit (Ambion) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Total RNA was isolated using a RiboPureTM -Bacteria Kit (Ambion) following the manufacturer’s instructions. Once isolated, ~10μg total RNA was treated with 8 units DNase (Invitrogen) twice to remove genomic DNA. PGCGROWTHCONDITIONS
Transform the mapped file format from sam to sorted bam which are later tranfered to bigWig, and separated by the strand (plus and minus). PGCGROWTHCONDITIONS
culture/growth condition: Heatshock 15min PGCGROWTHCONDITIONS
E. coli cells_HS15min PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For the Illumina GAII platform, the directional RNA-seq libraries were constructed by following an Illumina’s instruction using their Small RNA Sample Prep Kit with some modifications. For the HiSeq 2000 platform, the directional RNA-seq libraries were constructed using Illumina’s TruSeq Small RNA Sample Prep Kit. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K12 str MG1655 PGCGROWTHCONDITIONS
HS15min_r3_GAII PGCGROWTHCONDITIONS
Merge the replicates for each sample. For example, for sample HS15min, merge HS15min_r1.HiSeq.fastq.gz, HS15min_r2.HiSeq.fastq.gz and HS15min_r3.HiSeq.fastq.gz to one fastq file PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, then mapped to E. coli K12 genome using bowtie v0.12.7 with parameters bowtie -t -v 3 -m 1 --best -S -p 2 PGCGROWTHCONDITIONS
strain: K12 PGCGROWTHCONDITIONS
substrain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWig files for whole-genome reads coverage (including number of mapped reads) for each sample. Each sample has two files, one for plus strand, and the other for minus strand. Therefore, there are 14 BigWig files for 7 samples. PGCGROWTHCONDITIONS
To enrich mRNAs and other transcripts, majority of rRNAs were removed from the DNase-treated total RNA using a MICROBExpress kit (Ambion) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Total RNA was isolated using a RiboPureTM -Bacteria Kit (Ambion) following the manufacturer’s instructions. Once isolated, ~10μg total RNA was treated with 8 units DNase (Invitrogen) twice to remove genomic DNA. PGCGROWTHCONDITIONS
Transform the mapped file format from sam to sorted bam which are later tranfered to bigWig, and separated by the strand (plus and minus). PGCGROWTHCONDITIONS
culture/growth condition: Heatshock 30min PGCGROWTHCONDITIONS
E. coli cells_HS30min PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For the Illumina GAII platform, the directional RNA-seq libraries were constructed by following an Illumina’s instruction using their Small RNA Sample Prep Kit with some modifications. For the HiSeq 2000 platform, the directional RNA-seq libraries were constructed using Illumina’s TruSeq Small RNA Sample Prep Kit. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K12 str MG1655 PGCGROWTHCONDITIONS
HS30min_r1_HiSeq PGCGROWTHCONDITIONS
Merge the replicates for each sample. For example, for sample HS15min, merge HS15min_r1.HiSeq.fastq.gz, HS15min_r2.HiSeq.fastq.gz and HS15min_r3.HiSeq.fastq.gz to one fastq file PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, then mapped to E. coli K12 genome using bowtie v0.12.7 with parameters bowtie -t -v 3 -m 1 --best -S -p 2 PGCGROWTHCONDITIONS
strain: K12 PGCGROWTHCONDITIONS
substrain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWig files for whole-genome reads coverage (including number of mapped reads) for each sample. Each sample has two files, one for plus strand, and the other for minus strand. Therefore, there are 14 BigWig files for 7 samples. PGCGROWTHCONDITIONS
To enrich mRNAs and other transcripts, majority of rRNAs were removed from the DNase-treated total RNA using a MICROBExpress kit (Ambion) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Total RNA was isolated using a RiboPureTM -Bacteria Kit (Ambion) following the manufacturer’s instructions. Once isolated, ~10μg total RNA was treated with 8 units DNase (Invitrogen) twice to remove genomic DNA. PGCGROWTHCONDITIONS
Transform the mapped file format from sam to sorted bam which are later tranfered to bigWig, and separated by the strand (plus and minus). PGCGROWTHCONDITIONS
culture/growth condition: Heatshock 30min PGCGROWTHCONDITIONS
E. coli cells_HS30min PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For the Illumina GAII platform, the directional RNA-seq libraries were constructed by following an Illumina’s instruction using their Small RNA Sample Prep Kit with some modifications. For the HiSeq 2000 platform, the directional RNA-seq libraries were constructed using Illumina’s TruSeq Small RNA Sample Prep Kit. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K12 str MG1655 PGCGROWTHCONDITIONS
HS30min_r2_HiSeq PGCGROWTHCONDITIONS
Merge the replicates for each sample. For example, for sample HS15min, merge HS15min_r1.HiSeq.fastq.gz, HS15min_r2.HiSeq.fastq.gz and HS15min_r3.HiSeq.fastq.gz to one fastq file PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, then mapped to E. coli K12 genome using bowtie v0.12.7 with parameters bowtie -t -v 3 -m 1 --best -S -p 2 PGCGROWTHCONDITIONS
strain: K12 PGCGROWTHCONDITIONS
substrain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWig files for whole-genome reads coverage (including number of mapped reads) for each sample. Each sample has two files, one for plus strand, and the other for minus strand. Therefore, there are 14 BigWig files for 7 samples. PGCGROWTHCONDITIONS
To enrich mRNAs and other transcripts, majority of rRNAs were removed from the DNase-treated total RNA using a MICROBExpress kit (Ambion) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Total RNA was isolated using a RiboPureTM -Bacteria Kit (Ambion) following the manufacturer’s instructions. Once isolated, ~10μg total RNA was treated with 8 units DNase (Invitrogen) twice to remove genomic DNA. PGCGROWTHCONDITIONS
Transform the mapped file format from sam to sorted bam which are later tranfered to bigWig, and separated by the strand (plus and minus). PGCGROWTHCONDITIONS
culture/growth condition: Heatshock 60min PGCGROWTHCONDITIONS
E. coli cells_HS60min PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For the Illumina GAII platform, the directional RNA-seq libraries were constructed by following an Illumina’s instruction using their Small RNA Sample Prep Kit with some modifications. For the HiSeq 2000 platform, the directional RNA-seq libraries were constructed using Illumina’s TruSeq Small RNA Sample Prep Kit. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K12 str MG1655 PGCGROWTHCONDITIONS
HS60min_r1_HiSeq PGCGROWTHCONDITIONS
Merge the replicates for each sample. For example, for sample HS15min, merge HS15min_r1.HiSeq.fastq.gz, HS15min_r2.HiSeq.fastq.gz and HS15min_r3.HiSeq.fastq.gz to one fastq file PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, then mapped to E. coli K12 genome using bowtie v0.12.7 with parameters bowtie -t -v 3 -m 1 --best -S -p 2 PGCGROWTHCONDITIONS
strain: K12 PGCGROWTHCONDITIONS
substrain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWig files for whole-genome reads coverage (including number of mapped reads) for each sample. Each sample has two files, one for plus strand, and the other for minus strand. Therefore, there are 14 BigWig files for 7 samples. PGCGROWTHCONDITIONS
To enrich mRNAs and other transcripts, majority of rRNAs were removed from the DNase-treated total RNA using a MICROBExpress kit (Ambion) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Total RNA was isolated using a RiboPureTM -Bacteria Kit (Ambion) following the manufacturer’s instructions. Once isolated, ~10μg total RNA was treated with 8 units DNase (Invitrogen) twice to remove genomic DNA. PGCGROWTHCONDITIONS
Transform the mapped file format from sam to sorted bam which are later tranfered to bigWig, and separated by the strand (plus and minus). PGCGROWTHCONDITIONS
culture/growth condition: Heatshock 60min PGCGROWTHCONDITIONS
E. coli cells_HS60min PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For the Illumina GAII platform, the directional RNA-seq libraries were constructed by following an Illumina’s instruction using their Small RNA Sample Prep Kit with some modifications. For the HiSeq 2000 platform, the directional RNA-seq libraries were constructed using Illumina’s TruSeq Small RNA Sample Prep Kit. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K12 str MG1655 PGCGROWTHCONDITIONS
HS60min_r2_HiSeq PGCGROWTHCONDITIONS
Merge the replicates for each sample. For example, for sample HS15min, merge HS15min_r1.HiSeq.fastq.gz, HS15min_r2.HiSeq.fastq.gz and HS15min_r3.HiSeq.fastq.gz to one fastq file PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, then mapped to E. coli K12 genome using bowtie v0.12.7 with parameters bowtie -t -v 3 -m 1 --best -S -p 2 PGCGROWTHCONDITIONS
strain: K12 PGCGROWTHCONDITIONS
substrain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWig files for whole-genome reads coverage (including number of mapped reads) for each sample. Each sample has two files, one for plus strand, and the other for minus strand. Therefore, there are 14 BigWig files for 7 samples. PGCGROWTHCONDITIONS
To enrich mRNAs and other transcripts, majority of rRNAs were removed from the DNase-treated total RNA using a MICROBExpress kit (Ambion) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Total RNA was isolated using a RiboPureTM -Bacteria Kit (Ambion) following the manufacturer’s instructions. Once isolated, ~10μg total RNA was treated with 8 units DNase (Invitrogen) twice to remove genomic DNA. PGCGROWTHCONDITIONS
Transform the mapped file format from sam to sorted bam which are later tranfered to bigWig, and separated by the strand (plus and minus). PGCGROWTHCONDITIONS
culture/growth condition: MOPS-P 0h PGCGROWTHCONDITIONS
E. coli cells_M-P0h PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For the Illumina GAII platform, the directional RNA-seq libraries were constructed by following an Illumina’s instruction using their Small RNA Sample Prep Kit with some modifications. For the HiSeq 2000 platform, the directional RNA-seq libraries were constructed using Illumina’s TruSeq Small RNA Sample Prep Kit. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K12 str MG1655 PGCGROWTHCONDITIONS
Merge the replicates for each sample. For example, for sample HS15min, merge HS15min_r1.HiSeq.fastq.gz, HS15min_r2.HiSeq.fastq.gz and HS15min_r3.HiSeq.fastq.gz to one fastq file PGCGROWTHCONDITIONS
M-P0h_r1_HiSeq PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, then mapped to E. coli K12 genome using bowtie v0.12.7 with parameters bowtie -t -v 3 -m 1 --best -S -p 2 PGCGROWTHCONDITIONS
strain: K12 PGCGROWTHCONDITIONS
substrain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWig files for whole-genome reads coverage (including number of mapped reads) for each sample. Each sample has two files, one for plus strand, and the other for minus strand. Therefore, there are 14 BigWig files for 7 samples. PGCGROWTHCONDITIONS
To enrich mRNAs and other transcripts, majority of rRNAs were removed from the DNase-treated total RNA using a MICROBExpress kit (Ambion) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Total RNA was isolated using a RiboPureTM -Bacteria Kit (Ambion) following the manufacturer’s instructions. Once isolated, ~10μg total RNA was treated with 8 units DNase (Invitrogen) twice to remove genomic DNA. PGCGROWTHCONDITIONS
Transform the mapped file format from sam to sorted bam which are later tranfered to bigWig, and separated by the strand (plus and minus). PGCGROWTHCONDITIONS
culture/growth condition: MOPS-P 0h PGCGROWTHCONDITIONS
E. coli cells_M-P0h PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For the Illumina GAII platform, the directional RNA-seq libraries were constructed by following an Illumina’s instruction using their Small RNA Sample Prep Kit with some modifications. For the HiSeq 2000 platform, the directional RNA-seq libraries were constructed using Illumina’s TruSeq Small RNA Sample Prep Kit. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K12 str MG1655 PGCGROWTHCONDITIONS
Merge the replicates for each sample. For example, for sample HS15min, merge HS15min_r1.HiSeq.fastq.gz, HS15min_r2.HiSeq.fastq.gz and HS15min_r3.HiSeq.fastq.gz to one fastq file PGCGROWTHCONDITIONS
M-P0h_r2_HiSeq PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, then mapped to E. coli K12 genome using bowtie v0.12.7 with parameters bowtie -t -v 3 -m 1 --best -S -p 2 PGCGROWTHCONDITIONS
strain: K12 PGCGROWTHCONDITIONS
substrain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWig files for whole-genome reads coverage (including number of mapped reads) for each sample. Each sample has two files, one for plus strand, and the other for minus strand. Therefore, there are 14 BigWig files for 7 samples. PGCGROWTHCONDITIONS
To enrich mRNAs and other transcripts, majority of rRNAs were removed from the DNase-treated total RNA using a MICROBExpress kit (Ambion) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Total RNA was isolated using a RiboPureTM -Bacteria Kit (Ambion) following the manufacturer’s instructions. Once isolated, ~10μg total RNA was treated with 8 units DNase (Invitrogen) twice to remove genomic DNA. PGCGROWTHCONDITIONS
Transform the mapped file format from sam to sorted bam which are later tranfered to bigWig, and separated by the strand (plus and minus). PGCGROWTHCONDITIONS
culture/growth condition: MOPS-P 2h PGCGROWTHCONDITIONS
E. coli cells_M-P2h PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For the Illumina GAII platform, the directional RNA-seq libraries were constructed by following an Illumina’s instruction using their Small RNA Sample Prep Kit with some modifications. For the HiSeq 2000 platform, the directional RNA-seq libraries were constructed using Illumina’s TruSeq Small RNA Sample Prep Kit. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K12 str MG1655 PGCGROWTHCONDITIONS
Merge the replicates for each sample. For example, for sample HS15min, merge HS15min_r1.HiSeq.fastq.gz, HS15min_r2.HiSeq.fastq.gz and HS15min_r3.HiSeq.fastq.gz to one fastq file PGCGROWTHCONDITIONS
M-P2h_r1_HiSeq PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, then mapped to E. coli K12 genome using bowtie v0.12.7 with parameters bowtie -t -v 3 -m 1 --best -S -p 2 PGCGROWTHCONDITIONS
strain: K12 PGCGROWTHCONDITIONS
substrain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWig files for whole-genome reads coverage (including number of mapped reads) for each sample. Each sample has two files, one for plus strand, and the other for minus strand. Therefore, there are 14 BigWig files for 7 samples. PGCGROWTHCONDITIONS
To enrich mRNAs and other transcripts, majority of rRNAs were removed from the DNase-treated total RNA using a MICROBExpress kit (Ambion) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Total RNA was isolated using a RiboPureTM -Bacteria Kit (Ambion) following the manufacturer’s instructions. Once isolated, ~10μg total RNA was treated with 8 units DNase (Invitrogen) twice to remove genomic DNA. PGCGROWTHCONDITIONS
Transform the mapped file format from sam to sorted bam which are later tranfered to bigWig, and separated by the strand (plus and minus). PGCGROWTHCONDITIONS
culture/growth condition: MOPS-P 2h PGCGROWTHCONDITIONS
E. coli cells_M-P2h PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For the Illumina GAII platform, the directional RNA-seq libraries were constructed by following an Illumina’s instruction using their Small RNA Sample Prep Kit with some modifications. For the HiSeq 2000 platform, the directional RNA-seq libraries were constructed using Illumina’s TruSeq Small RNA Sample Prep Kit. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K12 str MG1655 PGCGROWTHCONDITIONS
Merge the replicates for each sample. For example, for sample HS15min, merge HS15min_r1.HiSeq.fastq.gz, HS15min_r2.HiSeq.fastq.gz and HS15min_r3.HiSeq.fastq.gz to one fastq file PGCGROWTHCONDITIONS
M-P2h_r2_HiSeq PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, then mapped to E. coli K12 genome using bowtie v0.12.7 with parameters bowtie -t -v 3 -m 1 --best -S -p 2 PGCGROWTHCONDITIONS
strain: K12 PGCGROWTHCONDITIONS
substrain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWig files for whole-genome reads coverage (including number of mapped reads) for each sample. Each sample has two files, one for plus strand, and the other for minus strand. Therefore, there are 14 BigWig files for 7 samples. PGCGROWTHCONDITIONS
To enrich mRNAs and other transcripts, majority of rRNAs were removed from the DNase-treated total RNA using a MICROBExpress kit (Ambion) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Total RNA was isolated using a RiboPureTM -Bacteria Kit (Ambion) following the manufacturer’s instructions. Once isolated, ~10μg total RNA was treated with 8 units DNase (Invitrogen) twice to remove genomic DNA. PGCGROWTHCONDITIONS
Transform the mapped file format from sam to sorted bam which are later tranfered to bigWig, and separated by the strand (plus and minus). PGCGROWTHCONDITIONS
culture/growth condition: MOPS-P 4h PGCGROWTHCONDITIONS
E. coli cells_M-P4h PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For the Illumina GAII platform, the directional RNA-seq libraries were constructed by following an Illumina’s instruction using their Small RNA Sample Prep Kit with some modifications. For the HiSeq 2000 platform, the directional RNA-seq libraries were constructed using Illumina’s TruSeq Small RNA Sample Prep Kit. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K12 str MG1655 PGCGROWTHCONDITIONS
Merge the replicates for each sample. For example, for sample HS15min, merge HS15min_r1.HiSeq.fastq.gz, HS15min_r2.HiSeq.fastq.gz and HS15min_r3.HiSeq.fastq.gz to one fastq file PGCGROWTHCONDITIONS
M-P4h_r1_HiSeq PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, then mapped to E. coli K12 genome using bowtie v0.12.7 with parameters bowtie -t -v 3 -m 1 --best -S -p 2 PGCGROWTHCONDITIONS
strain: K12 PGCGROWTHCONDITIONS
substrain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWig files for whole-genome reads coverage (including number of mapped reads) for each sample. Each sample has two files, one for plus strand, and the other for minus strand. Therefore, there are 14 BigWig files for 7 samples. PGCGROWTHCONDITIONS
To enrich mRNAs and other transcripts, majority of rRNAs were removed from the DNase-treated total RNA using a MICROBExpress kit (Ambion) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Total RNA was isolated using a RiboPureTM -Bacteria Kit (Ambion) following the manufacturer’s instructions. Once isolated, ~10μg total RNA was treated with 8 units DNase (Invitrogen) twice to remove genomic DNA. PGCGROWTHCONDITIONS
Transform the mapped file format from sam to sorted bam which are later tranfered to bigWig, and separated by the strand (plus and minus). PGCGROWTHCONDITIONS
culture/growth condition: MOPS-P 4h PGCGROWTHCONDITIONS
E. coli cells_M-P4h PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For the Illumina GAII platform, the directional RNA-seq libraries were constructed by following an Illumina’s instruction using their Small RNA Sample Prep Kit with some modifications. For the HiSeq 2000 platform, the directional RNA-seq libraries were constructed using Illumina’s TruSeq Small RNA Sample Prep Kit. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K12 str MG1655 PGCGROWTHCONDITIONS
Merge the replicates for each sample. For example, for sample HS15min, merge HS15min_r1.HiSeq.fastq.gz, HS15min_r2.HiSeq.fastq.gz and HS15min_r3.HiSeq.fastq.gz to one fastq file PGCGROWTHCONDITIONS
M-P4h_r2_HiSeq PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, then mapped to E. coli K12 genome using bowtie v0.12.7 with parameters bowtie -t -v 3 -m 1 --best -S -p 2 PGCGROWTHCONDITIONS
strain: K12 PGCGROWTHCONDITIONS
substrain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWig files for whole-genome reads coverage (including number of mapped reads) for each sample. Each sample has two files, one for plus strand, and the other for minus strand. Therefore, there are 14 BigWig files for 7 samples. PGCGROWTHCONDITIONS
To enrich mRNAs and other transcripts, majority of rRNAs were removed from the DNase-treated total RNA using a MICROBExpress kit (Ambion) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Total RNA was isolated using a RiboPureTM -Bacteria Kit (Ambion) following the manufacturer’s instructions. Once isolated, ~10μg total RNA was treated with 8 units DNase (Invitrogen) twice to remove genomic DNA. PGCGROWTHCONDITIONS
Transform the mapped file format from sam to sorted bam which are later tranfered to bigWig, and separated by the strand (plus and minus). PGCGROWTHCONDITIONS
culture/growth condition: MOPS-P 4h PGCGROWTHCONDITIONS
E. coli cells_M-P4h PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For the Illumina GAII platform, the directional RNA-seq libraries were constructed by following an Illumina’s instruction using their Small RNA Sample Prep Kit with some modifications. For the HiSeq 2000 platform, the directional RNA-seq libraries were constructed using Illumina’s TruSeq Small RNA Sample Prep Kit. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K12 str MG1655 PGCGROWTHCONDITIONS
Merge the replicates for each sample. For example, for sample HS15min, merge HS15min_r1.HiSeq.fastq.gz, HS15min_r2.HiSeq.fastq.gz and HS15min_r3.HiSeq.fastq.gz to one fastq file PGCGROWTHCONDITIONS
M-P4h_r3_HiSeq PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, then mapped to E. coli K12 genome using bowtie v0.12.7 with parameters bowtie -t -v 3 -m 1 --best -S -p 2 PGCGROWTHCONDITIONS
strain: K12 PGCGROWTHCONDITIONS
substrain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWig files for whole-genome reads coverage (including number of mapped reads) for each sample. Each sample has two files, one for plus strand, and the other for minus strand. Therefore, there are 14 BigWig files for 7 samples. PGCGROWTHCONDITIONS
To enrich mRNAs and other transcripts, majority of rRNAs were removed from the DNase-treated total RNA using a MICROBExpress kit (Ambion) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Total RNA was isolated using a RiboPureTM -Bacteria Kit (Ambion) following the manufacturer’s instructions. Once isolated, ~10μg total RNA was treated with 8 units DNase (Invitrogen) twice to remove genomic DNA. PGCGROWTHCONDITIONS
Transform the mapped file format from sam to sorted bam which are later tranfered to bigWig, and separated by the strand (plus and minus). PGCGROWTHCONDITIONS
basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS
Differential expression analysis was carried out using cuffdiff v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
FPKM were calculated using Cufflinks v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS
growth stage: mid exponetial phase PGCGROWTHCONDITIONS
Illumina read were aligned to NC_000913 using Bowtie 1 with 2 mismatches allowed per read alignment PGCGROWTHCONDITIONS
Mid log cultures were treated with Qiagen RNA Protect reagent following the vendor's protocol. Cells were centrifuged and stored at -80 °C for <30 days prior to use. PGCGROWTHCONDITIONS
Mid log_wildtype_glc minimal media_aerobic rep1 PGCGROWTHCONDITIONS
oxygen condition: aerobic PGCGROWTHCONDITIONS
Paired-end, strand-specific RNAseq libraries were generated using the dUTP method {Levin JZ et al. 2010, Nat Methods} with the following modifications. rRNA was removed with Epicentre’s Ribo-Zero rRNA Removal Kit. Subtracted RNA was fragmented for 3 min using Ambion’s RNA Fragmentation Reagents. cDNA was generated using Invitrogen’s SuperScript III First-Strand Synthesis protocol with random hexamer priming. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: csv files, FPKM values from pairwise comparisons PGCGROWTHCONDITIONS
supplementation: None PGCGROWTHCONDITIONS
Total RNA was isolated using the Rneasy Mini Kit procedure with on column Dnase treatment (Qiagen). PGCGROWTHCONDITIONS
WT PGCGROWTHCONDITIONS
basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS
Differential expression analysis was carried out using cuffdiff v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
FPKM were calculated using Cufflinks v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS
growth stage: mid exponetial phase PGCGROWTHCONDITIONS
Illumina read were aligned to NC_000913 using Bowtie 1 with 2 mismatches allowed per read alignment PGCGROWTHCONDITIONS
Mid log cultures were treated with Qiagen RNA Protect reagent following the vendor's protocol. Cells were centrifuged and stored at -80 °C for <30 days prior to use. PGCGROWTHCONDITIONS
Mid log_wildtype_glc minimal media_aerobic rep2 PGCGROWTHCONDITIONS
oxygen condition: aerobic PGCGROWTHCONDITIONS
Paired-end, strand-specific RNAseq libraries were generated using the dUTP method {Levin JZ et al. 2010, Nat Methods} with the following modifications. rRNA was removed with Epicentre’s Ribo-Zero rRNA Removal Kit. Subtracted RNA was fragmented for 3 min using Ambion’s RNA Fragmentation Reagents. cDNA was generated using Invitrogen’s SuperScript III First-Strand Synthesis protocol with random hexamer priming. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: csv files, FPKM values from pairwise comparisons PGCGROWTHCONDITIONS
supplementation: None PGCGROWTHCONDITIONS
Total RNA was isolated using the Rneasy Mini Kit procedure with on column Dnase treatment (Qiagen). PGCGROWTHCONDITIONS
WT PGCGROWTHCONDITIONS
basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS
Differential expression analysis was carried out using cuffdiff v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
FPKM were calculated using Cufflinks v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS
growth stage: mid exponetial phase PGCGROWTHCONDITIONS
Illumina read were aligned to NC_000913 using Bowtie 1 with 2 mismatches allowed per read alignment PGCGROWTHCONDITIONS
Mid log cultures were treated with Qiagen RNA Protect reagent following the vendor's protocol. Cells were centrifuged and stored at -80 °C for <30 days prior to use. PGCGROWTHCONDITIONS
Mid log_wildtype_glc minimal media_aerobic rep3 PGCGROWTHCONDITIONS
oxygen condition: aerobic PGCGROWTHCONDITIONS
Paired-end, strand-specific RNAseq libraries were generated using the dUTP method {Levin JZ et al. 2010, Nat Methods} with the following modifications. rRNA was removed with Epicentre’s Ribo-Zero rRNA Removal Kit. Subtracted RNA was fragmented for 3 min using Ambion’s RNA Fragmentation Reagents. cDNA was generated using Invitrogen’s SuperScript III First-Strand Synthesis protocol with random hexamer priming. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: csv files, FPKM values from pairwise comparisons PGCGROWTHCONDITIONS
supplementation: None PGCGROWTHCONDITIONS
Total RNA was isolated using the Rneasy Mini Kit procedure with on column Dnase treatment (Qiagen). PGCGROWTHCONDITIONS
WT PGCGROWTHCONDITIONS
basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS
Differential expression analysis was carried out using cuffdiff v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
FPKM were calculated using Cufflinks v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS
growth stage: mid exponetial phase PGCGROWTHCONDITIONS
Illumina read were aligned to NC_000913 using Bowtie 1 with 2 mismatches allowed per read alignment PGCGROWTHCONDITIONS
Mid log cultures were treated with Qiagen RNA Protect reagent following the vendor's protocol. Cells were centrifuged and stored at -80 °C for <30 days prior to use. PGCGROWTHCONDITIONS
Mid log_wildtype_glc minimal media + adenine_aerobic PGCGROWTHCONDITIONS
oxygen condition: aerobic PGCGROWTHCONDITIONS
Paired-end, strand-specific RNAseq libraries were generated using the dUTP method {Levin JZ et al. 2010, Nat Methods} with the following modifications. rRNA was removed with Epicentre’s Ribo-Zero rRNA Removal Kit. Subtracted RNA was fragmented for 3 min using Ambion’s RNA Fragmentation Reagents. cDNA was generated using Invitrogen’s SuperScript III First-Strand Synthesis protocol with random hexamer priming. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: csv files, FPKM values from pairwise comparisons PGCGROWTHCONDITIONS
supplementation: adenine (10 mM) PGCGROWTHCONDITIONS
Total RNA was isolated using the Rneasy Mini Kit procedure with on column Dnase treatment (Qiagen). PGCGROWTHCONDITIONS
WT + ade PGCGROWTHCONDITIONS
basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS
Differential expression analysis was carried out using cuffdiff v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
FPKM were calculated using Cufflinks v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS
growth stage: mid exponetial phase PGCGROWTHCONDITIONS
Illumina read were aligned to NC_000913 using Bowtie 1 with 2 mismatches allowed per read alignment PGCGROWTHCONDITIONS
Mid log cultures were treated with Qiagen RNA Protect reagent following the vendor's protocol. Cells were centrifuged and stored at -80 °C for <30 days prior to use. PGCGROWTHCONDITIONS
Mid log_wildtype_glc minimal media + L-tryptophan_aerobic PGCGROWTHCONDITIONS
oxygen condition: aerobic PGCGROWTHCONDITIONS
Paired-end, strand-specific RNAseq libraries were generated using the dUTP method {Levin JZ et al. 2010, Nat Methods} with the following modifications. rRNA was removed with Epicentre’s Ribo-Zero rRNA Removal Kit. Subtracted RNA was fragmented for 3 min using Ambion’s RNA Fragmentation Reagents. cDNA was generated using Invitrogen’s SuperScript III First-Strand Synthesis protocol with random hexamer priming. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: csv files, FPKM values from pairwise comparisons PGCGROWTHCONDITIONS
supplementation: L-tryptophan (20 mg/L) PGCGROWTHCONDITIONS
Total RNA was isolated using the Rneasy Mini Kit procedure with on column Dnase treatment (Qiagen). PGCGROWTHCONDITIONS
WT + L-trp PGCGROWTHCONDITIONS
basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS
Differential expression analysis was carried out using cuffdiff v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
FPKM were calculated using Cufflinks v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS
growth stage: mid exponetial phase PGCGROWTHCONDITIONS
Illumina read were aligned to NC_000913 using Bowtie 1 with 2 mismatches allowed per read alignment PGCGROWTHCONDITIONS
Mid log cultures were treated with Qiagen RNA Protect reagent following the vendor's protocol. Cells were centrifuged and stored at -80 °C for <30 days prior to use. PGCGROWTHCONDITIONS
Mid log_wildtype_glc minimal media_anaerobic rep1 PGCGROWTHCONDITIONS
oxygen condition: anaerobic PGCGROWTHCONDITIONS
Paired-end, strand-specific RNAseq libraries were generated using the dUTP method {Levin JZ et al. 2010, Nat Methods} with the following modifications. rRNA was removed with Epicentre’s Ribo-Zero rRNA Removal Kit. Subtracted RNA was fragmented for 3 min using Ambion’s RNA Fragmentation Reagents. cDNA was generated using Invitrogen’s SuperScript III First-Strand Synthesis protocol with random hexamer priming. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: csv files, FPKM values from pairwise comparisons PGCGROWTHCONDITIONS
supplementation: None PGCGROWTHCONDITIONS
Total RNA was isolated using the Rneasy Mini Kit procedure with on column Dnase treatment (Qiagen). PGCGROWTHCONDITIONS
WT -O2 PGCGROWTHCONDITIONS
basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS
Differential expression analysis was carried out using cuffdiff v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
FPKM were calculated using Cufflinks v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS
growth stage: mid exponetial phase PGCGROWTHCONDITIONS
Illumina read were aligned to NC_000913 using Bowtie 1 with 2 mismatches allowed per read alignment PGCGROWTHCONDITIONS
Mid log cultures were treated with Qiagen RNA Protect reagent following the vendor's protocol. Cells were centrifuged and stored at -80 °C for <30 days prior to use. PGCGROWTHCONDITIONS
Mid log_wildtype_glc minimal media_anaerobic rep2 PGCGROWTHCONDITIONS
oxygen condition: anaerobic PGCGROWTHCONDITIONS
Paired-end, strand-specific RNAseq libraries were generated using the dUTP method {Levin JZ et al. 2010, Nat Methods} with the following modifications. rRNA was removed with Epicentre’s Ribo-Zero rRNA Removal Kit. Subtracted RNA was fragmented for 3 min using Ambion’s RNA Fragmentation Reagents. cDNA was generated using Invitrogen’s SuperScript III First-Strand Synthesis protocol with random hexamer priming. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: csv files, FPKM values from pairwise comparisons PGCGROWTHCONDITIONS
supplementation: None PGCGROWTHCONDITIONS
Total RNA was isolated using the Rneasy Mini Kit procedure with on column Dnase treatment (Qiagen). PGCGROWTHCONDITIONS
WT -O2 PGCGROWTHCONDITIONS
basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS
Differential expression analysis was carried out using cuffdiff v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
FPKM were calculated using Cufflinks v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS
growth stage: mid exponetial phase PGCGROWTHCONDITIONS
Illumina read were aligned to NC_000913 using Bowtie 1 with 2 mismatches allowed per read alignment PGCGROWTHCONDITIONS
Mid log cultures were treated with Qiagen RNA Protect reagent following the vendor's protocol. Cells were centrifuged and stored at -80 °C for <30 days prior to use. PGCGROWTHCONDITIONS
Mid log_wildtype_glc minimal media_anaerobic rep3 PGCGROWTHCONDITIONS
oxygen condition: anaerobic PGCGROWTHCONDITIONS
Paired-end, strand-specific RNAseq libraries were generated using the dUTP method {Levin JZ et al. 2010, Nat Methods} with the following modifications. rRNA was removed with Epicentre’s Ribo-Zero rRNA Removal Kit. Subtracted RNA was fragmented for 3 min using Ambion’s RNA Fragmentation Reagents. cDNA was generated using Invitrogen’s SuperScript III First-Strand Synthesis protocol with random hexamer priming. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: csv files, FPKM values from pairwise comparisons PGCGROWTHCONDITIONS
supplementation: None PGCGROWTHCONDITIONS
Total RNA was isolated using the Rneasy Mini Kit procedure with on column Dnase treatment (Qiagen). PGCGROWTHCONDITIONS
WT -O2 PGCGROWTHCONDITIONS
basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS
Differential expression analysis was carried out using cuffdiff v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
FPKM were calculated using Cufflinks v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
genotype/variation: nac KO; BW25113 Dnac PGCGROWTHCONDITIONS
growth stage: mid exponetial phase PGCGROWTHCONDITIONS
Illumina read were aligned to NC_000913 using Bowtie 1 with 2 mismatches allowed per read alignment PGCGROWTHCONDITIONS
Mid log cultures were treated with Qiagen RNA Protect reagent following the vendor's protocol. Cells were centrifuged and stored at -80 °C for <30 days prior to use. PGCGROWTHCONDITIONS
Mid log_nac KO_glc minimal media_aerobic PGCGROWTHCONDITIONS
nac KO PGCGROWTHCONDITIONS
oxygen condition: aerobic PGCGROWTHCONDITIONS
Paired-end, strand-specific RNAseq libraries were generated using the dUTP method {Levin JZ et al. 2010, Nat Methods} with the following modifications. rRNA was removed with Epicentre’s Ribo-Zero rRNA Removal Kit. Subtracted RNA was fragmented for 3 min using Ambion’s RNA Fragmentation Reagents. cDNA was generated using Invitrogen’s SuperScript III First-Strand Synthesis protocol with random hexamer priming. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: csv files, FPKM values from pairwise comparisons PGCGROWTHCONDITIONS
supplementation: None PGCGROWTHCONDITIONS
Total RNA was isolated using the Rneasy Mini Kit procedure with on column Dnase treatment (Qiagen). PGCGROWTHCONDITIONS
basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS
Differential expression analysis was carried out using cuffdiff v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
FPKM were calculated using Cufflinks v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
genotype/variation: nac KO; BW25113 Dnac PGCGROWTHCONDITIONS
growth stage: mid exponetial phase PGCGROWTHCONDITIONS
Illumina read were aligned to NC_000913 using Bowtie 1 with 2 mismatches allowed per read alignment PGCGROWTHCONDITIONS
Mid log cultures were treated with Qiagen RNA Protect reagent following the vendor's protocol. Cells were centrifuged and stored at -80 °C for <30 days prior to use. PGCGROWTHCONDITIONS
Mid log_nac KO_glc minimal media + adenine_aerobic PGCGROWTHCONDITIONS
nac KO + ade PGCGROWTHCONDITIONS
oxygen condition: aerobic PGCGROWTHCONDITIONS
Paired-end, strand-specific RNAseq libraries were generated using the dUTP method {Levin JZ et al. 2010, Nat Methods} with the following modifications. rRNA was removed with Epicentre’s Ribo-Zero rRNA Removal Kit. Subtracted RNA was fragmented for 3 min using Ambion’s RNA Fragmentation Reagents. cDNA was generated using Invitrogen’s SuperScript III First-Strand Synthesis protocol with random hexamer priming. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: csv files, FPKM values from pairwise comparisons PGCGROWTHCONDITIONS
supplementation: adenine (10 mM) PGCGROWTHCONDITIONS
Total RNA was isolated using the Rneasy Mini Kit procedure with on column Dnase treatment (Qiagen). PGCGROWTHCONDITIONS
basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS
cra KO PGCGROWTHCONDITIONS
Differential expression analysis was carried out using cuffdiff v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
FPKM were calculated using Cufflinks v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
genotype/variation: cra KO; BW25113 Dcra PGCGROWTHCONDITIONS
growth stage: mid exponetial phase PGCGROWTHCONDITIONS
Illumina read were aligned to NC_000913 using Bowtie 1 with 2 mismatches allowed per read alignment PGCGROWTHCONDITIONS
Mid log_cra KO_glc minimal media_aerobic PGCGROWTHCONDITIONS
Mid log cultures were treated with Qiagen RNA Protect reagent following the vendor's protocol. Cells were centrifuged and stored at -80 °C for <30 days prior to use. PGCGROWTHCONDITIONS
oxygen condition: aerobic PGCGROWTHCONDITIONS
Paired-end, strand-specific RNAseq libraries were generated using the dUTP method {Levin JZ et al. 2010, Nat Methods} with the following modifications. rRNA was removed with Epicentre’s Ribo-Zero rRNA Removal Kit. Subtracted RNA was fragmented for 3 min using Ambion’s RNA Fragmentation Reagents. cDNA was generated using Invitrogen’s SuperScript III First-Strand Synthesis protocol with random hexamer priming. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: csv files, FPKM values from pairwise comparisons PGCGROWTHCONDITIONS
supplementation: None PGCGROWTHCONDITIONS
Total RNA was isolated using the Rneasy Mini Kit procedure with on column Dnase treatment (Qiagen). PGCGROWTHCONDITIONS
basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS
cra KO + L-trp PGCGROWTHCONDITIONS
Differential expression analysis was carried out using cuffdiff v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
FPKM were calculated using Cufflinks v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
genotype/variation: cra KO; BW25113 Dcra PGCGROWTHCONDITIONS
growth stage: mid exponetial phase PGCGROWTHCONDITIONS
Illumina read were aligned to NC_000913 using Bowtie 1 with 2 mismatches allowed per read alignment PGCGROWTHCONDITIONS
Mid log_cra KO_glc minimal media + L-tryptophan_aerobic PGCGROWTHCONDITIONS
Mid log cultures were treated with Qiagen RNA Protect reagent following the vendor's protocol. Cells were centrifuged and stored at -80 °C for <30 days prior to use. PGCGROWTHCONDITIONS
oxygen condition: aerobic PGCGROWTHCONDITIONS
Paired-end, strand-specific RNAseq libraries were generated using the dUTP method {Levin JZ et al. 2010, Nat Methods} with the following modifications. rRNA was removed with Epicentre’s Ribo-Zero rRNA Removal Kit. Subtracted RNA was fragmented for 3 min using Ambion’s RNA Fragmentation Reagents. cDNA was generated using Invitrogen’s SuperScript III First-Strand Synthesis protocol with random hexamer priming. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: csv files, FPKM values from pairwise comparisons PGCGROWTHCONDITIONS
supplementation: L-tryptophan (20 mg/L) PGCGROWTHCONDITIONS
Total RNA was isolated using the Rneasy Mini Kit procedure with on column Dnase treatment (Qiagen). PGCGROWTHCONDITIONS
basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS
Differential expression analysis was carried out using cuffdiff v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
FPKM were calculated using Cufflinks v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
genotype/variation: mntR KO; BW25113 DmntR PGCGROWTHCONDITIONS
growth stage: mid exponetial phase PGCGROWTHCONDITIONS
Illumina read were aligned to NC_000913 using Bowtie 1 with 2 mismatches allowed per read alignment PGCGROWTHCONDITIONS
Mid log cultures were treated with Qiagen RNA Protect reagent following the vendor's protocol. Cells were centrifuged and stored at -80 °C for <30 days prior to use. PGCGROWTHCONDITIONS
Mid log_mntR KO_glc minimal media_aerobic PGCGROWTHCONDITIONS
mntR KO PGCGROWTHCONDITIONS
oxygen condition: aerobic PGCGROWTHCONDITIONS
Paired-end, strand-specific RNAseq libraries were generated using the dUTP method {Levin JZ et al. 2010, Nat Methods} with the following modifications. rRNA was removed with Epicentre’s Ribo-Zero rRNA Removal Kit. Subtracted RNA was fragmented for 3 min using Ambion’s RNA Fragmentation Reagents. cDNA was generated using Invitrogen’s SuperScript III First-Strand Synthesis protocol with random hexamer priming. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: csv files, FPKM values from pairwise comparisons PGCGROWTHCONDITIONS
supplementation: None PGCGROWTHCONDITIONS
Total RNA was isolated using the Rneasy Mini Kit procedure with on column Dnase treatment (Qiagen). PGCGROWTHCONDITIONS
basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS
Differential expression analysis was carried out using cuffdiff v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
FPKM were calculated using Cufflinks v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
genotype/variation: mntR KO; BW25113 DmntR PGCGROWTHCONDITIONS
growth stage: mid exponetial phase PGCGROWTHCONDITIONS
Illumina read were aligned to NC_000913 using Bowtie 1 with 2 mismatches allowed per read alignment PGCGROWTHCONDITIONS
Mid log cultures were treated with Qiagen RNA Protect reagent following the vendor's protocol. Cells were centrifuged and stored at -80 °C for <30 days prior to use. PGCGROWTHCONDITIONS
Mid log_mntR KO_glc minimal media_anaerobic PGCGROWTHCONDITIONS
mntR KO -O2 PGCGROWTHCONDITIONS
oxygen condition: anaerobic PGCGROWTHCONDITIONS
Paired-end, strand-specific RNAseq libraries were generated using the dUTP method {Levin JZ et al. 2010, Nat Methods} with the following modifications. rRNA was removed with Epicentre’s Ribo-Zero rRNA Removal Kit. Subtracted RNA was fragmented for 3 min using Ambion’s RNA Fragmentation Reagents. cDNA was generated using Invitrogen’s SuperScript III First-Strand Synthesis protocol with random hexamer priming. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: csv files, FPKM values from pairwise comparisons PGCGROWTHCONDITIONS
supplementation: None PGCGROWTHCONDITIONS
Total RNA was isolated using the Rneasy Mini Kit procedure with on column Dnase treatment (Qiagen). PGCGROWTHCONDITIONS
23A1 PGCGROWTHCONDITIONS
23A1 PGCGROWTHCONDITIONS
DNA was extracted in the same manner as described by McNulty et al. (PMID: 22030749). PGCGROWTHCONDITIONS
ecoli NC_000913.2 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: ASM584v1 PGCGROWTHCONDITIONS
genotype/variation: ydcR (b1439) MUTANT PGCGROWTHCONDITIONS
Illumina Casava software used for basecalling. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome using bowtie2 version 2.0.5 with default parameters. PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample. PGCGROWTHCONDITIONS
23B1 PGCGROWTHCONDITIONS
23B1 PGCGROWTHCONDITIONS
DNA was extracted in the same manner as described by McNulty et al. (PMID: 22030749). PGCGROWTHCONDITIONS
ecoli NC_000913.2 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: ASM584v1 PGCGROWTHCONDITIONS
genotype/variation: ydcR (b1439) MUTANT PGCGROWTHCONDITIONS
Illumina Casava software used for basecalling. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome using bowtie2 version 2.0.5 with default parameters. PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample. PGCGROWTHCONDITIONS
23C3 PGCGROWTHCONDITIONS
23C3 PGCGROWTHCONDITIONS
DNA was extracted in the same manner as described by McNulty et al. (PMID: 22030749). PGCGROWTHCONDITIONS
ecoli NC_000913.2 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: ASM584v1 PGCGROWTHCONDITIONS
genotype/variation: ydcR (b1439) MUTANT PGCGROWTHCONDITIONS
Illumina Casava software used for basecalling. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome using bowtie2 version 2.0.5 with default parameters. PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample. PGCGROWTHCONDITIONS
39A1 PGCGROWTHCONDITIONS
39A1 PGCGROWTHCONDITIONS
DNA was extracted in the same manner as described by McNulty et al. (PMID: 22030749). PGCGROWTHCONDITIONS
ecoli NC_000913.2 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: ASM584v1 PGCGROWTHCONDITIONS
genotype/variation: yjiR (b4340) MUTANT PGCGROWTHCONDITIONS
Illumina Casava software used for basecalling. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome using bowtie2 version 2.0.5 with default parameters. PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample. PGCGROWTHCONDITIONS
39B1 PGCGROWTHCONDITIONS
39B1 PGCGROWTHCONDITIONS
DNA was extracted in the same manner as described by McNulty et al. (PMID: 22030749). PGCGROWTHCONDITIONS
ecoli NC_000913.2 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: ASM584v1 PGCGROWTHCONDITIONS
genotype/variation: yjiR (b4340) MUTANT PGCGROWTHCONDITIONS
Illumina Casava software used for basecalling. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome using bowtie2 version 2.0.5 with default parameters. PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample. PGCGROWTHCONDITIONS
39C1 PGCGROWTHCONDITIONS
39C1 PGCGROWTHCONDITIONS
DNA was extracted in the same manner as described by McNulty et al. (PMID: 22030749). PGCGROWTHCONDITIONS
ecoli NC_000913.2 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: ASM584v1 PGCGROWTHCONDITIONS
genotype/variation: yjiR (b4340) MUTANT PGCGROWTHCONDITIONS
Illumina Casava software used for basecalling. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome using bowtie2 version 2.0.5 with default parameters. PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample. PGCGROWTHCONDITIONS
DNA was extracted in the same manner as described by McNulty et al. (PMID: 22030749). PGCGROWTHCONDITIONS
ecoli NC_000913.2 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: ASM584v1 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
Illumina Casava software used for basecalling. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome using bowtie2 version 2.0.5 with default parameters. PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample. PGCGROWTHCONDITIONS
WTA1 PGCGROWTHCONDITIONS
WTA1 PGCGROWTHCONDITIONS
DNA was extracted in the same manner as described by McNulty et al. (PMID: 22030749). PGCGROWTHCONDITIONS
ecoli NC_000913.2 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: ASM584v1 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
Illumina Casava software used for basecalling. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome using bowtie2 version 2.0.5 with default parameters. PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample. PGCGROWTHCONDITIONS
WTB1 PGCGROWTHCONDITIONS
WTB1 PGCGROWTHCONDITIONS
DNA was extracted in the same manner as described by McNulty et al. (PMID: 22030749). PGCGROWTHCONDITIONS
ecoli NC_000913.2 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: ASM584v1 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
Illumina Casava software used for basecalling. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome using bowtie2 version 2.0.5 with default parameters. PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample. PGCGROWTHCONDITIONS
WTC3 PGCGROWTHCONDITIONS
WTC3 PGCGROWTHCONDITIONS
All cultures were based on MOPS media with 0.2% glucose (Teknova), with either full supplement (Neidhardt et al., 1974). An overnight liquid culture was diluted 400-fold into 200 ml fresh media. The culture was kept in a 2.8-liter flask at 37C with aeration (180 rpm) until OD600 reached 0.3. PGCGROWTHCONDITIONS
bacteria PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E coli genome were converted to wiggle files. The position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011). 200 ml of cell culture was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C. PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
media: fully supplemented MOPS glucose media PGCGROWTHCONDITIONS
mRNA-seq in rich defined media PGCGROWTHCONDITIONS
Ribosome protected mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More at G.W. Li, D. Burkhardt, C.A. Gross, J. S. Weissman (Cell). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
EC_Cont1_RNA PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For all the samples; when 1/3 of the maximum OD600 was reached, cells were harvested by centrifugation (7,500 rcf for 5 min) and frozen. For RNA isolation, cells were lysed by bead beating and RNA was purified using phenol-chloroform extractions and ethanol precipitations. DNA was removed from the sample with RNase-free DNase I (Fermentas) treatment for 45 min. Ribolock (Fermentas) was added to avoid RNA degradation. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K-12, substr. MG1655 (assembly ASM584v2) PGCGROWTHCONDITIONS
Genome_build: Streptococcus pneumoniae D39 (assembly ASM1436v1) PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
Illumina Casava 1.8 software was used for basecalling. PGCGROWTHCONDITIONS
Library preparation was performed by vertis Biotechnologie AG, according to the following protocol: RNA samples were first treated with rDNase. From the total RNA samples, ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Removal Kit (Bacteria, Epicentre). the rRNA depleted RNA samples were fragmented with ultrasound (2 pulses of 30 sec at 4°C). Firststrand cDNA synthesis was primed with a N6 randomized primer. Then, Illumina TruSeq sequencing adapters were ligated to the 5' and 3' ends of the cDNA. The cDNA was finally amplified with PCR (16-18 cycles, depending on sample) using a proof reading enzyme. Aliquots of each library were analyzed by capillary electrophoresis. PGCGROWTHCONDITIONS
molecule subtype: total RNA, rRNA depleted PGCGROWTHCONDITIONS
Overnight cultures of strain JM83 were diluted 1/100 in LB medium and grown in microtiter plates. To study the effects of trimethoprim, cells grown without antibiotics were compared to cells grown with 0.5 μg/ml trimethoprim. PGCGROWTHCONDITIONS
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. For the S. pneumoniae samples this was done internally by Rockhopper version 1.21 after aligning reads. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
S. pneumoniae reads were mapped to the D39 whole genome with Rockhopper version 1.21, using default parameters. E. coli reads were mapped to the K-12, substr. MG1655 whole genome with Bowtie 2, using parameters --mixed --discordant -D 10 -R 2 -N 0 -L 22 -i S,0,2.50. PGCGROWTHCONDITIONS
strain: JM83 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample. PGCGROWTHCONDITIONS
treated with: none (untreated control) PGCGROWTHCONDITIONS
Untreated E. coli cells PGCGROWTHCONDITIONS
EC_Cont2_RNA PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For all the samples; when 1/3 of the maximum OD600 was reached, cells were harvested by centrifugation (7,500 rcf for 5 min) and frozen. For RNA isolation, cells were lysed by bead beating and RNA was purified using phenol-chloroform extractions and ethanol precipitations. DNA was removed from the sample with RNase-free DNase I (Fermentas) treatment for 45 min. Ribolock (Fermentas) was added to avoid RNA degradation. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K-12, substr. MG1655 (assembly ASM584v2) PGCGROWTHCONDITIONS
Genome_build: Streptococcus pneumoniae D39 (assembly ASM1436v1) PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
Illumina Casava 1.8 software was used for basecalling. PGCGROWTHCONDITIONS
Library preparation was performed by vertis Biotechnologie AG, according to the following protocol: RNA samples were first treated with rDNase. From the total RNA samples, ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Removal Kit (Bacteria, Epicentre). the rRNA depleted RNA samples were fragmented with ultrasound (2 pulses of 30 sec at 4°C). Firststrand cDNA synthesis was primed with a N6 randomized primer. Then, Illumina TruSeq sequencing adapters were ligated to the 5' and 3' ends of the cDNA. The cDNA was finally amplified with PCR (16-18 cycles, depending on sample) using a proof reading enzyme. Aliquots of each library were analyzed by capillary electrophoresis. PGCGROWTHCONDITIONS
molecule subtype: total RNA, rRNA depleted PGCGROWTHCONDITIONS
Overnight cultures of strain JM83 were diluted 1/100 in LB medium and grown in microtiter plates. To study the effects of trimethoprim, cells grown without antibiotics were compared to cells grown with 0.5 μg/ml trimethoprim. PGCGROWTHCONDITIONS
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. For the S. pneumoniae samples this was done internally by Rockhopper version 1.21 after aligning reads. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
S. pneumoniae reads were mapped to the D39 whole genome with Rockhopper version 1.21, using default parameters. E. coli reads were mapped to the K-12, substr. MG1655 whole genome with Bowtie 2, using parameters --mixed --discordant -D 10 -R 2 -N 0 -L 22 -i S,0,2.50. PGCGROWTHCONDITIONS
strain: JM83 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample. PGCGROWTHCONDITIONS
treated with: none (untreated control) PGCGROWTHCONDITIONS
Untreated E. coli cells PGCGROWTHCONDITIONS
EC_Trim1_RNA PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For all the samples; when 1/3 of the maximum OD600 was reached, cells were harvested by centrifugation (7,500 rcf for 5 min) and frozen. For RNA isolation, cells were lysed by bead beating and RNA was purified using phenol-chloroform extractions and ethanol precipitations. DNA was removed from the sample with RNase-free DNase I (Fermentas) treatment for 45 min. Ribolock (Fermentas) was added to avoid RNA degradation. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K-12, substr. MG1655 (assembly ASM584v2) PGCGROWTHCONDITIONS
Genome_build: Streptococcus pneumoniae D39 (assembly ASM1436v1) PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
Illumina Casava 1.8 software was used for basecalling. PGCGROWTHCONDITIONS
Library preparation was performed by vertis Biotechnologie AG, according to the following protocol: RNA samples were first treated with rDNase. From the total RNA samples, ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Removal Kit (Bacteria, Epicentre). the rRNA depleted RNA samples were fragmented with ultrasound (2 pulses of 30 sec at 4°C). Firststrand cDNA synthesis was primed with a N6 randomized primer. Then, Illumina TruSeq sequencing adapters were ligated to the 5' and 3' ends of the cDNA. The cDNA was finally amplified with PCR (16-18 cycles, depending on sample) using a proof reading enzyme. Aliquots of each library were analyzed by capillary electrophoresis. PGCGROWTHCONDITIONS
molecule subtype: total RNA, rRNA depleted PGCGROWTHCONDITIONS
Overnight cultures of strain JM83 were diluted 1/100 in LB medium and grown in microtiter plates. To study the effects of trimethoprim, cells grown without antibiotics were compared to cells grown with 0.5 μg/ml trimethoprim. PGCGROWTHCONDITIONS
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. For the S. pneumoniae samples this was done internally by Rockhopper version 1.21 after aligning reads. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
S. pneumoniae reads were mapped to the D39 whole genome with Rockhopper version 1.21, using default parameters. E. coli reads were mapped to the K-12, substr. MG1655 whole genome with Bowtie 2, using parameters --mixed --discordant -D 10 -R 2 -N 0 -L 22 -i S,0,2.50. PGCGROWTHCONDITIONS
strain: JM83 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample. PGCGROWTHCONDITIONS
treated with: 0.5 μg/ml trimethoprim PGCGROWTHCONDITIONS
Trimethoprim-treated E. coli cells PGCGROWTHCONDITIONS
EC_Trim2_RNA PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For all the samples; when 1/3 of the maximum OD600 was reached, cells were harvested by centrifugation (7,500 rcf for 5 min) and frozen. For RNA isolation, cells were lysed by bead beating and RNA was purified using phenol-chloroform extractions and ethanol precipitations. DNA was removed from the sample with RNase-free DNase I (Fermentas) treatment for 45 min. Ribolock (Fermentas) was added to avoid RNA degradation. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K-12, substr. MG1655 (assembly ASM584v2) PGCGROWTHCONDITIONS
Genome_build: Streptococcus pneumoniae D39 (assembly ASM1436v1) PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
Illumina Casava 1.8 software was used for basecalling. PGCGROWTHCONDITIONS
Library preparation was performed by vertis Biotechnologie AG, according to the following protocol: RNA samples were first treated with rDNase. From the total RNA samples, ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Removal Kit (Bacteria, Epicentre). the rRNA depleted RNA samples were fragmented with ultrasound (2 pulses of 30 sec at 4°C). Firststrand cDNA synthesis was primed with a N6 randomized primer. Then, Illumina TruSeq sequencing adapters were ligated to the 5' and 3' ends of the cDNA. The cDNA was finally amplified with PCR (16-18 cycles, depending on sample) using a proof reading enzyme. Aliquots of each library were analyzed by capillary electrophoresis. PGCGROWTHCONDITIONS
molecule subtype: total RNA, rRNA depleted PGCGROWTHCONDITIONS
Overnight cultures of strain JM83 were diluted 1/100 in LB medium and grown in microtiter plates. To study the effects of trimethoprim, cells grown without antibiotics were compared to cells grown with 0.5 μg/ml trimethoprim. PGCGROWTHCONDITIONS
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. For the S. pneumoniae samples this was done internally by Rockhopper version 1.21 after aligning reads. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
S. pneumoniae reads were mapped to the D39 whole genome with Rockhopper version 1.21, using default parameters. E. coli reads were mapped to the K-12, substr. MG1655 whole genome with Bowtie 2, using parameters --mixed --discordant -D 10 -R 2 -N 0 -L 22 -i S,0,2.50. PGCGROWTHCONDITIONS
strain: JM83 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample. PGCGROWTHCONDITIONS
treated with: 0.5 μg/ml trimethoprim PGCGROWTHCONDITIONS
Trimethoprim-treated E. coli cells PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: no ethanol exposure PGCGROWTHCONDITIONS
Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: No PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Wild-type (MG1655) T0 RNA rep 2 PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: 40 g EtOH/L, 10 min PGCGROWTHCONDITIONS
Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: No PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Wild-type (MG1655) T1 RNA rep 1 PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: 40 g EtOH/L, 10 min PGCGROWTHCONDITIONS
Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: No PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Wild-type (MG1655) T1 RNA rep 2 PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: 40 g EtOH/L, 70 min PGCGROWTHCONDITIONS
Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: No PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Wild-type (MG1655) T2 RNA rep 1 PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: 40 g EtOH/L, 70 min PGCGROWTHCONDITIONS
Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: No PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Wild-type (MG1655) T2 RNA rep 2 PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: no ethanol exposure PGCGROWTHCONDITIONS
Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Mutant (EP61) T0 RNA rep 1 PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: No PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: EP61 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: no ethanol exposure PGCGROWTHCONDITIONS
Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Mutant (EP61) T0 RNA rep 2 PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: No PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: EP61 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: 40 g EtOH/L, 10 min PGCGROWTHCONDITIONS
Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Mutant (EP61) T1 RNA rep 1 PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: No PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: EP61 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: 40 g EtOH/L, 10 min PGCGROWTHCONDITIONS
Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Mutant (EP61) T1 RNA rep 2 PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: No PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: EP61 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: 40 g EtOH/L, 70 min PGCGROWTHCONDITIONS
Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Mutant (EP61) T2 RNA rep 1 PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: No PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: EP61 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: 40 g EtOH/L, 70 min PGCGROWTHCONDITIONS
Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Mutant (EP61) T2 RNA rep 2 PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: No PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: EP61 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: no ethanol exposure PGCGROWTHCONDITIONS
Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: Yes PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Wild-type (MG1655) T0 RP rep 1 PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: no ethanol exposure PGCGROWTHCONDITIONS
Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: Yes PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Wild-type (MG1655) T0 RP rep 2 PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: 40 g EtOH/L, 10 min PGCGROWTHCONDITIONS
Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: Yes PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Wild-type (MG1655) T1 RP rep 1 PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: 40 g EtOH/L, 10 min PGCGROWTHCONDITIONS
Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: Yes PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Wild-type (MG1655) T1 RP rep 2 PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: 40 g EtOH/L, 70 min PGCGROWTHCONDITIONS
Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: Yes PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Wild-type (MG1655) T2 RP rep 1 PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: 40 g EtOH/L, 70 min PGCGROWTHCONDITIONS
Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: Yes PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Wild-type (MG1655) T2 RP rep 2 PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: no ethanol exposure PGCGROWTHCONDITIONS
Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Mutant (EP61) T0 RP rep 1 PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: Yes PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: EP61 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: no ethanol exposure PGCGROWTHCONDITIONS
Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Mutant (EP61) T0 RP rep 2 PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: Yes PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: EP61 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: 40 g EtOH/L, 10 min PGCGROWTHCONDITIONS
Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Mutant (EP61) T1 RP rep 1 PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: Yes PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: EP61 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: 40 g EtOH/L, 10 min PGCGROWTHCONDITIONS
Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Mutant (EP61) T1 RP rep 2 PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: Yes PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: EP61 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: 40 g EtOH/L, 70 min PGCGROWTHCONDITIONS
Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Mutant (EP61) T2 RP rep 1 PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: Yes PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: EP61 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
ethanol treatment: 40 g EtOH/L, 70 min PGCGROWTHCONDITIONS
Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the ll genes\ dataset (see supplementary file for list of genes in ll genes\, \low ribosome occupancy\, and \high ribosome occupancy\ gene sets) PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
Mutant (EP61) T2 RP rep 2 PGCGROWTHCONDITIONS
Raw reads were trimmed by two nt from the 5' end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
ribosome-protected: Yes PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
strain: EP61 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a \-\ as the final character in the file name cover the minus strand of the genome; those with a \+\ as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.7 PGCGROWTHCONDITIONS
Cells were grown in MOPS minimal medium with 0.2% glucose at 37 degrees C in gas-sparged Roux bottles to mid-log phase. PGCGROWTHCONDITIONS
Culture samples were transferred directly into an ice-cold ethanol/phenol stop solution, then collected by centrifugation and stored at -80°C until RNA extraction. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: ASM584v1, U00096.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Parkhomchuk et al. 2009, Nucleic Acids Res 37: e123. Briefly, ribosome-depleted RNA was fragmented and used as template for cDNA synhtesis. dUTP was included in the second strand synthesis reaction in addition to dTTP to chemically mark the second strand. cDNAs were size-selected and ligated to sequencing adapters followed by dUTP cleavage to generate adapter-ligated single-stranded cDNAs. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-seq reads were mapped to the E. coli K-12 MG1655 genome (GenBank ID U00096.2) using short oligonucleotide alignment program (SOAP) PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files normalized to reads per million per position.  Those designated \minus\ cover the minus strand of the genome; those with designated \plus\ cover the plus strand of the genome. PGCGROWTHCONDITIONS
Wild-type (MG1655) RNA-seq PGCGROWTHCONDITIONS
Aerobic culture PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.7 PGCGROWTHCONDITIONS
Cells were grown in MOPS minimal medium with 0.2% glucose at 37 degrees C in gas-sparged Roux bottles to mid-log phase. PGCGROWTHCONDITIONS
Culture samples were transferred directly into an ice-cold ethanol/phenol stop solution, then collected by centrifugation and stored at -80°C until RNA extraction. PGCGROWTHCONDITIONS
Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: ASM584v1, U00096.2 PGCGROWTHCONDITIONS
Library construction was performed as described in Parkhomchuk et al. 2009, Nucleic Acids Res 37: e123. Briefly, ribosome-depleted RNA was fragmented and used as template for cDNA synhtesis. dUTP was included in the second strand synthesis reaction in addition to dTTP to chemically mark the second strand. cDNAs were size-selected and ligated to sequencing adapters followed by dUTP cleavage to generate adapter-ligated single-stranded cDNAs. PGCGROWTHCONDITIONS
Mutant (RL2325) RNA-seq PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-seq reads were mapped to the E. coli K-12 MG1655 genome (GenBank ID U00096.2) using short oligonucleotide alignment program (SOAP) PGCGROWTHCONDITIONS
RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
strain: RL2325 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data files are WIG files normalized to reads per million per position.  Those designated \minus\ cover the minus strand of the genome; those with designated \plus\ cover the plus strand of the genome. PGCGROWTHCONDITIONS
Bacteria PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the reference genome were converted to wiggle files. The position of each alignment was mapped to the 3' end of the nascent transcript. PGCGROWTHCONDITIONS
Cell culture was rapidly filtered in 250 mL increments at 37 °C over 0.22 μm nitrocellulose filters (GE) and frozen in liquid nitrogen to simultaneously halt all transcriptional progress. Frozen cells (100 μg) were pulverized on a Qiagen TissueLyser II mixer mill 6 times at 15 Hz for 3 min in the presence of 500 μL frozen lysis buffer (20 mM Tris pH 8, 0.4% Triton X-100, 0.1% NP-40, 100 mM NH4Cl, 50 U/mL SUPERase•In (Ambion)) and 1X protease inhibitor cocktail (Complete, EDTA-free, Roche), supplemented with 10 mM MnCl2. The lysate was resuspended on ice by pipetting. RQ1 DNase I (110 U total, Promega) was added and incubated for 20 min on ice. The reaction was quenched with EDTA (25 mM final), which releases polysomes from the transcript and reduces contamination from ribosomal RNA and ribosome-associated tRNAs. The lysate was clarified at 4 °C by centrifugation at 20,000 g for 10 min. The lysate was loaded onto a PD MiniTrap G-25 column (GE Healthcare) and eluted with lysis buffer supplemented with 1 mM EDTA. Total RNA was purified from the clarified lysate using the miRNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Ecoli_WT_RNAseq PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For each sample, 500 mL liquid cultures were grown in 2.8 L flasks with shaking (180 rpm) at 37 °C from an OD (600 nm) 0.05 to OD 0.45 ± 0.05. Cells were grown in MOPS EZ rich defined medium with 0.2% glucose (Teknova). PGCGROWTHCONDITIONS
Genome_build: E. coli: NC_000913 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
media: MOPS EZ Rich Defined Media PGCGROWTHCONDITIONS
molecule subtype: Total RNA PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain background: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
The full library construction protocol was described in detail previously (Churchman et al., Nature 2011). Purified total RNA was fragmented and dephosphorylated with T4 PNK, and then ligated to a 5' adenylated DNA oligo to generate RNA ranging from 30-100 nt. The RNA was reverse transcribed, and the single-stranded DNA circularized and PCR amplified. PGCGROWTHCONDITIONS
Trimmed reads were aligned using Bowtie v0.12.7 against the reference genome using parameters -a -v 3 -m 1 PGCGROWTHCONDITIONS
All cultures grown up to 0.6 OD600 with shaking at 200 rpm. Samples 1,2,5 and 6 were grown at 30°C whereas samples 3 and 4 were grown at 37°C. PGCGROWTHCONDITIONS
analysis: in vivo PGCGROWTHCONDITIONS
Basecalls were performed using CASAVA.1.8 PGCGROWTHCONDITIONS
Cultures for samples 1 and 2 were incubated at 44°C for 45 min after growth. PGCGROWTHCONDITIONS
E. coli cell cultures PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: U00096.2 PGCGROWTHCONDITIONS
genotype: rne wild-type PGCGROWTHCONDITIONS
incubation time: n/a PGCGROWTHCONDITIONS
Libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rne wild-type PGCGROWTHCONDITIONS
Sequence reads were trimmed for adaptor reads and mapped to E. coli K12 MG1655 genome using CLC Genomics Workbench 6.0.1 PGCGROWTHCONDITIONS
strain: N3433 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed files are in tab delimited format. Separate files are provided for the forward and reverse strands. The start and end coordinates should be the same. Each line in the data set represents the position of the first nucleotide at the 5' end of a sequence that could be mapped to the E. coli genome. PGCGROWTHCONDITIONS
Total RNA was isolated as desribed in Kime et al., 2008 PGCGROWTHCONDITIONS
All cultures grown up to 0.6 OD600 with shaking at 200 rpm. Samples 1,2,5 and 6 were grown at 30°C whereas samples 3 and 4 were grown at 37°C. PGCGROWTHCONDITIONS
analysis: in vivo PGCGROWTHCONDITIONS
Basecalls were performed using CASAVA.1.8 PGCGROWTHCONDITIONS
Cultures for samples 1 and 2 were incubated at 44°C for 45 min after growth. PGCGROWTHCONDITIONS
E. coli cell cultures PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: U00096.2 PGCGROWTHCONDITIONS
genotype: rne-3071 (ts) PGCGROWTHCONDITIONS
incubation time: n/a PGCGROWTHCONDITIONS
Libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rne-3071 ts PGCGROWTHCONDITIONS
Sequence reads were trimmed for adaptor reads and mapped to E. coli K12 MG1655 genome using CLC Genomics Workbench 6.0.1 PGCGROWTHCONDITIONS
strain: N3431 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed files are in tab delimited format. Separate files are provided for the forward and reverse strands. The start and end coordinates should be the same. Each line in the data set represents the position of the first nucleotide at the 5' end of a sequence that could be mapped to the E. coli genome. PGCGROWTHCONDITIONS
Total RNA was isolated as desribed in Kime et al., 2008 PGCGROWTHCONDITIONS
All cultures grown up to 0.6 OD600 with shaking at 200 rpm. Samples 1,2,5 and 6 were grown at 30°C whereas samples 3 and 4 were grown at 37°C. PGCGROWTHCONDITIONS
analysis: in vitro PGCGROWTHCONDITIONS
Basecalls were performed using CASAVA.1.8 PGCGROWTHCONDITIONS
Cultures for samples 1 and 2 were incubated at 44°C for 45 min after growth. PGCGROWTHCONDITIONS
E. coli cell cultures PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: U00096.2 PGCGROWTHCONDITIONS
genotype: n/a PGCGROWTHCONDITIONS
incubation time: 0 min PGCGROWTHCONDITIONS
Libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequence reads were trimmed for adaptor reads and mapped to E. coli K12 MG1655 genome using CLC Genomics Workbench 6.0.1 PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed files are in tab delimited format. Separate files are provided for the forward and reverse strands. The start and end coordinates should be the same. Each line in the data set represents the position of the first nucleotide at the 5' end of a sequence that could be mapped to the E. coli genome. PGCGROWTHCONDITIONS
T170V 0 min PGCGROWTHCONDITIONS
Total RNA was isolated as desribed in Kime et al., 2008 PGCGROWTHCONDITIONS
All cultures grown up to 0.6 OD600 with shaking at 200 rpm. Samples 1,2,5 and 6 were grown at 30°C whereas samples 3 and 4 were grown at 37°C. PGCGROWTHCONDITIONS
analysis: in vitro PGCGROWTHCONDITIONS
Basecalls were performed using CASAVA.1.8 PGCGROWTHCONDITIONS
Cultures for samples 1 and 2 were incubated at 44°C for 45 min after growth. PGCGROWTHCONDITIONS
E. coli cell cultures PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: U00096.2 PGCGROWTHCONDITIONS
genotype: n/a PGCGROWTHCONDITIONS
incubation time: 10 min PGCGROWTHCONDITIONS
Libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequence reads were trimmed for adaptor reads and mapped to E. coli K12 MG1655 genome using CLC Genomics Workbench 6.0.1 PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed files are in tab delimited format. Separate files are provided for the forward and reverse strands. The start and end coordinates should be the same. Each line in the data set represents the position of the first nucleotide at the 5' end of a sequence that could be mapped to the E. coli genome. PGCGROWTHCONDITIONS
T170V 10 min PGCGROWTHCONDITIONS
Total RNA was isolated as desribed in Kime et al., 2008 PGCGROWTHCONDITIONS
All cultures grown up to 0.6 OD600 with shaking at 200 rpm. Samples 1,2,5 and 6 were grown at 30°C whereas samples 3 and 4 were grown at 37°C. PGCGROWTHCONDITIONS
analysis: in vivo PGCGROWTHCONDITIONS
Basecalls were performed using CASAVA.1.8 PGCGROWTHCONDITIONS
Cultures for samples 1 and 2 were incubated at 44°C for 45 min after growth. PGCGROWTHCONDITIONS
E. coli cell cultures PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: U00096.2 PGCGROWTHCONDITIONS
genotype: rng wild-type PGCGROWTHCONDITIONS
incubation time: n/a PGCGROWTHCONDITIONS
Libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rng wild-type PGCGROWTHCONDITIONS
Sequence reads were trimmed for adaptor reads and mapped to E. coli K12 MG1655 genome using CLC Genomics Workbench 6.0.1 PGCGROWTHCONDITIONS
strain: MC1061 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed files are in tab delimited format. Separate files are provided for the forward and reverse strands. The start and end coordinates should be the same. Each line in the data set represents the position of the first nucleotide at the 5' end of a sequence that could be mapped to the E. coli genome. PGCGROWTHCONDITIONS
Total RNA was isolated as desribed in Kime et al., 2008 PGCGROWTHCONDITIONS
All cultures grown up to 0.6 OD600 with shaking at 200 rpm. Samples 1,2,5 and 6 were grown at 30°C whereas samples 3 and 4 were grown at 37°C. PGCGROWTHCONDITIONS
analysis: in vivo PGCGROWTHCONDITIONS
Basecalls were performed using CASAVA.1.8 PGCGROWTHCONDITIONS
Cultures for samples 1 and 2 were incubated at 44°C for 45 min after growth. PGCGROWTHCONDITIONS
E. coli cell cultures PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: U00096.2 PGCGROWTHCONDITIONS
genotype: rng mutant PGCGROWTHCONDITIONS
incubation time: n/a PGCGROWTHCONDITIONS
Libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rng mutant PGCGROWTHCONDITIONS
Sequence reads were trimmed for adaptor reads and mapped to E. coli K12 MG1655 genome using CLC Genomics Workbench 6.0.1 PGCGROWTHCONDITIONS
strain: GM11 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed files are in tab delimited format. Separate files are provided for the forward and reverse strands. The start and end coordinates should be the same. Each line in the data set represents the position of the first nucleotide at the 5' end of a sequence that could be mapped to the E. coli genome. PGCGROWTHCONDITIONS
Total RNA was isolated as desribed in Kime et al., 2008 PGCGROWTHCONDITIONS
All samples were extracted using the hot phenol extraction with DNA digestion, following standard protocol PGCGROWTHCONDITIONS
BigWIG files were viewed and annotated using Jbrowse and Integrated Genome Viewer. PGCGROWTHCONDITIONS
cDNA libraries were constructed at Vertis in Germany using a ligation based stratagey for Illumina whole transcriptome sequencing. Total RNA (DNase I digested) was fragmented by RNase III. RNA samples labeled as TEX were also subsequently digested with Terminator Exonuclease (TEX). Pyrophosphate groups were removed from the 5′ terminus using tobacco acid pyrophosphatase (TAP), and an RNA adapter was ligated to the 5′ end of the RNA. First-strand synthesis was performed using standard Illumina protocols. PGCGROWTHCONDITIONS
Cell culture PGCGROWTHCONDITIONS
Escherichia coli BW38028 PGCGROWTHCONDITIONS
For alignment of the reads contained within the fastq files to the E. coli MG1655 reference genome (RefSeq NC_U00096.3), the short read alignment tool Bowtie2 was utilized under default settings.  Bowtie parameters were set to include only perfect matches and map once reads that map to more than one genome location, i.e., uniquely mapped reads are retained. The output Bowtie2 was a SAM files for each sample. PGCGROWTHCONDITIONS
Genome_build: Reference genome for E. coli MG1655 (RefSeq NC_000913.3). PGCGROWTHCONDITIONS
genotype: wt PGCGROWTHCONDITIONS
growth phase: Log phase OD 0.4 PGCGROWTHCONDITIONS
Prior to total RNA extraction harvested bacterial cells were stored at -80.0°C in an equal volume of RNAlater. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample type: no RNA treatment PGCGROWTHCONDITIONS
Sequence data was processed by conversion of the sample alignment (BAM) files to strand-specific base count (BigWIG) files. To accomplish this an in-house script was created to extract strand-specific base count data from BAM files (outputs are positive and negative strand BigWIG files). PGCGROWTHCONDITIONS
strain: BW38028 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWIG files are provided showing uniquely mapped sequence reads. PGCGROWTHCONDITIONS
The data output from the Illumina Hiseq System was obtained directly from Vertis PGCGROWTHCONDITIONS
treatment: log phase sample PGCGROWTHCONDITIONS
Used SAMTOOLS (Li, et al., PMID 1950593) to sort and index the SAM files obtained from Bowtie2 and convert them to BAM format. PGCGROWTHCONDITIONS
Wild type E. coli K-12 (strain BW38038) and BW39452(ΔrpoS) cultures were grown on MOPS glucose minimal medium with 0.2% glucose as sole carbon source at 37°C, pH was initially 7.4,  and the agitation speed was 500 rpm. Culture samples were harvested during logarithmic growth and  following entry into stationary phase for the WT and rpoS mutant. OD600 measurements were made on a Beckman Coulter DU 800 spectrophotometer. Samples were harvested directly into ice-cold RNAlater at a 1:1 dilution to protect RNA from degradation and cells then were pelleted by centrifugation at 8000rpm for 10 minutes. Cell pellets were stored at -80°C in an equal volume of RNAlater prior to RNA extraction. PGCGROWTHCONDITIONS
WT_glucose_log PGCGROWTHCONDITIONS
All samples were extracted using the hot phenol extraction with DNA digestion, following standard protocol PGCGROWTHCONDITIONS
BigWIG files were viewed and annotated using Jbrowse and Integrated Genome Viewer. PGCGROWTHCONDITIONS
cDNA libraries were constructed at Vertis in Germany using a ligation based stratagey for Illumina whole transcriptome sequencing. Total RNA (DNase I digested) was fragmented by RNase III. RNA samples labeled as TEX were also subsequently digested with Terminator Exonuclease (TEX). Pyrophosphate groups were removed from the 5′ terminus using tobacco acid pyrophosphatase (TAP), and an RNA adapter was ligated to the 5′ end of the RNA. First-strand synthesis was performed using standard Illumina protocols. PGCGROWTHCONDITIONS
Cell culture PGCGROWTHCONDITIONS
Escherichia coli BW38028 PGCGROWTHCONDITIONS
For alignment of the reads contained within the fastq files to the E. coli MG1655 reference genome (RefSeq NC_U00096.3), the short read alignment tool Bowtie2 was utilized under default settings.  Bowtie parameters were set to include only perfect matches and map once reads that map to more than one genome location, i.e., uniquely mapped reads are retained. The output Bowtie2 was a SAM files for each sample. PGCGROWTHCONDITIONS
Genome_build: Reference genome for E. coli MG1655 (RefSeq NC_000913.3). PGCGROWTHCONDITIONS
genotype: wt PGCGROWTHCONDITIONS
growth phase: 30 min post stationary PGCGROWTHCONDITIONS
Prior to total RNA extraction harvested bacterial cells were stored at -80.0°C in an equal volume of RNAlater. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample type: no RNA treatment PGCGROWTHCONDITIONS
Sequence data was processed by conversion of the sample alignment (BAM) files to strand-specific base count (BigWIG) files. To accomplish this an in-house script was created to extract strand-specific base count data from BAM files (outputs are positive and negative strand BigWIG files). PGCGROWTHCONDITIONS
strain: BW38028 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWIG files are provided showing uniquely mapped sequence reads. PGCGROWTHCONDITIONS
The data output from the Illumina Hiseq System was obtained directly from Vertis PGCGROWTHCONDITIONS
treatment: Carbon starvation PGCGROWTHCONDITIONS
Used SAMTOOLS (Li, et al., PMID 1950593) to sort and index the SAM files obtained from Bowtie2 and convert them to BAM format. PGCGROWTHCONDITIONS
Wild type E. coli K-12 (strain BW38038) and BW39452(ΔrpoS) cultures were grown on MOPS glucose minimal medium with 0.2% glucose as sole carbon source at 37°C, pH was initially 7.4,  and the agitation speed was 500 rpm. Culture samples were harvested during logarithmic growth and  following entry into stationary phase for the WT and rpoS mutant. OD600 measurements were made on a Beckman Coulter DU 800 spectrophotometer. Samples were harvested directly into ice-cold RNAlater at a 1:1 dilution to protect RNA from degradation and cells then were pelleted by centrifugation at 8000rpm for 10 minutes. Cell pellets were stored at -80°C in an equal volume of RNAlater prior to RNA extraction. PGCGROWTHCONDITIONS
WT_glucose_stat PGCGROWTHCONDITIONS
All samples were extracted using the hot phenol extraction with DNA digestion, following standard protocol PGCGROWTHCONDITIONS
BigWIG files were viewed and annotated using Jbrowse and Integrated Genome Viewer. PGCGROWTHCONDITIONS
cDNA libraries were constructed at Vertis in Germany using a ligation based stratagey for Illumina whole transcriptome sequencing. Total RNA (DNase I digested) was fragmented by RNase III. RNA samples labeled as TEX were also subsequently digested with Terminator Exonuclease (TEX). Pyrophosphate groups were removed from the 5′ terminus using tobacco acid pyrophosphatase (TAP), and an RNA adapter was ligated to the 5′ end of the RNA. First-strand synthesis was performed using standard Illumina protocols. PGCGROWTHCONDITIONS
Cell culture PGCGROWTHCONDITIONS
Escherichia coli BW38028 PGCGROWTHCONDITIONS
For alignment of the reads contained within the fastq files to the E. coli MG1655 reference genome (RefSeq NC_U00096.3), the short read alignment tool Bowtie2 was utilized under default settings.  Bowtie parameters were set to include only perfect matches and map once reads that map to more than one genome location, i.e., uniquely mapped reads are retained. The output Bowtie2 was a SAM files for each sample. PGCGROWTHCONDITIONS
Genome_build: Reference genome for E. coli MG1655 (RefSeq NC_000913.3). PGCGROWTHCONDITIONS
genotype: wt PGCGROWTHCONDITIONS
growth phase: 30 min post stationary PGCGROWTHCONDITIONS
Prior to total RNA extraction harvested bacterial cells were stored at -80.0°C in an equal volume of RNAlater. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample type: no RNA treatment PGCGROWTHCONDITIONS
Sequence data was processed by conversion of the sample alignment (BAM) files to strand-specific base count (BigWIG) files. To accomplish this an in-house script was created to extract strand-specific base count data from BAM files (outputs are positive and negative strand BigWIG files). PGCGROWTHCONDITIONS
strain: BW38028 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWIG files are provided showing uniquely mapped sequence reads. PGCGROWTHCONDITIONS
The data output from the Illumina Hiseq System was obtained directly from Vertis PGCGROWTHCONDITIONS
treatment: Nitrogen starvation PGCGROWTHCONDITIONS
Used SAMTOOLS (Li, et al., PMID 1950593) to sort and index the SAM files obtained from Bowtie2 and convert them to BAM format. PGCGROWTHCONDITIONS
Wild type E. coli K-12 (strain BW38038) and BW39452(ΔrpoS) cultures were grown on MOPS glucose minimal medium with 0.2% glucose as sole carbon source at 37°C, pH was initially 7.4,  and the agitation speed was 500 rpm. Culture samples were harvested during logarithmic growth and  following entry into stationary phase for the WT and rpoS mutant. OD600 measurements were made on a Beckman Coulter DU 800 spectrophotometer. Samples were harvested directly into ice-cold RNAlater at a 1:1 dilution to protect RNA from degradation and cells then were pelleted by centrifugation at 8000rpm for 10 minutes. Cell pellets were stored at -80°C in an equal volume of RNAlater prior to RNA extraction. PGCGROWTHCONDITIONS
WT_N_strv PGCGROWTHCONDITIONS
All samples were extracted using the hot phenol extraction with DNA digestion, following standard protocol PGCGROWTHCONDITIONS
BigWIG files were viewed and annotated using Jbrowse and Integrated Genome Viewer. PGCGROWTHCONDITIONS
cDNA libraries were constructed at Vertis in Germany using a ligation based stratagey for Illumina whole transcriptome sequencing. Total RNA (DNase I digested) was fragmented by RNase III. RNA samples labeled as TEX were also subsequently digested with Terminator Exonuclease (TEX). Pyrophosphate groups were removed from the 5′ terminus using tobacco acid pyrophosphatase (TAP), and an RNA adapter was ligated to the 5′ end of the RNA. First-strand synthesis was performed using standard Illumina protocols. PGCGROWTHCONDITIONS
Cell culture PGCGROWTHCONDITIONS
Escherichia coli BW38028 PGCGROWTHCONDITIONS
For alignment of the reads contained within the fastq files to the E. coli MG1655 reference genome (RefSeq NC_U00096.3), the short read alignment tool Bowtie2 was utilized under default settings.  Bowtie parameters were set to include only perfect matches and map once reads that map to more than one genome location, i.e., uniquely mapped reads are retained. The output Bowtie2 was a SAM files for each sample. PGCGROWTHCONDITIONS
Genome_build: Reference genome for E. coli MG1655 (RefSeq NC_000913.3). PGCGROWTHCONDITIONS
genotype: rpoS PGCGROWTHCONDITIONS
growth phase: 30 min post stationary PGCGROWTHCONDITIONS
Prior to total RNA extraction harvested bacterial cells were stored at -80.0°C in an equal volume of RNAlater. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rpoS_N_strv PGCGROWTHCONDITIONS
sample type: no RNA treatment PGCGROWTHCONDITIONS
Sequence data was processed by conversion of the sample alignment (BAM) files to strand-specific base count (BigWIG) files. To accomplish this an in-house script was created to extract strand-specific base count data from BAM files (outputs are positive and negative strand BigWIG files). PGCGROWTHCONDITIONS
strain: BW38028 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWIG files are provided showing uniquely mapped sequence reads. PGCGROWTHCONDITIONS
The data output from the Illumina Hiseq System was obtained directly from Vertis PGCGROWTHCONDITIONS
treatment: Nitrogen starvation PGCGROWTHCONDITIONS
Used SAMTOOLS (Li, et al., PMID 1950593) to sort and index the SAM files obtained from Bowtie2 and convert them to BAM format. PGCGROWTHCONDITIONS
Wild type E. coli K-12 (strain BW38038) and BW39452(ΔrpoS) cultures were grown on MOPS glucose minimal medium with 0.2% glucose as sole carbon source at 37°C, pH was initially 7.4,  and the agitation speed was 500 rpm. Culture samples were harvested during logarithmic growth and  following entry into stationary phase for the WT and rpoS mutant. OD600 measurements were made on a Beckman Coulter DU 800 spectrophotometer. Samples were harvested directly into ice-cold RNAlater at a 1:1 dilution to protect RNA from degradation and cells then were pelleted by centrifugation at 8000rpm for 10 minutes. Cell pellets were stored at -80°C in an equal volume of RNAlater prior to RNA extraction. PGCGROWTHCONDITIONS
All samples were extracted using the hot phenol extraction with DNA digestion, following standard protocol PGCGROWTHCONDITIONS
BigWIG files were viewed and annotated using Jbrowse and Integrated Genome Viewer. PGCGROWTHCONDITIONS
cDNA libraries were constructed at Vertis in Germany using a ligation based stratagey for Illumina whole transcriptome sequencing. Total RNA (DNase I digested) was fragmented by RNase III. RNA samples labeled as TEX were also subsequently digested with Terminator Exonuclease (TEX). Pyrophosphate groups were removed from the 5′ terminus using tobacco acid pyrophosphatase (TAP), and an RNA adapter was ligated to the 5′ end of the RNA. First-strand synthesis was performed using standard Illumina protocols. PGCGROWTHCONDITIONS
Cell culture PGCGROWTHCONDITIONS
Escherichia coli BW38028 PGCGROWTHCONDITIONS
For alignment of the reads contained within the fastq files to the E. coli MG1655 reference genome (RefSeq NC_U00096.3), the short read alignment tool Bowtie2 was utilized under default settings.  Bowtie parameters were set to include only perfect matches and map once reads that map to more than one genome location, i.e., uniquely mapped reads are retained. The output Bowtie2 was a SAM files for each sample. PGCGROWTHCONDITIONS
Genome_build: Reference genome for E. coli MG1655 (RefSeq NC_000913.3). PGCGROWTHCONDITIONS
genotype: wt PGCGROWTHCONDITIONS
growth phase: Log phase OD 0.4 PGCGROWTHCONDITIONS
Prior to total RNA extraction harvested bacterial cells were stored at -80.0°C in an equal volume of RNAlater. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample type: no RNA treatment PGCGROWTHCONDITIONS
Sequence data was processed by conversion of the sample alignment (BAM) files to strand-specific base count (BigWIG) files. To accomplish this an in-house script was created to extract strand-specific base count data from BAM files (outputs are positive and negative strand BigWIG files). PGCGROWTHCONDITIONS
strain: BW38028 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWIG files are provided showing uniquely mapped sequence reads. PGCGROWTHCONDITIONS
The data output from the Illumina Hiseq System was obtained directly from Vertis PGCGROWTHCONDITIONS
treatment: log phase sample PGCGROWTHCONDITIONS
Used SAMTOOLS (Li, et al., PMID 1950593) to sort and index the SAM files obtained from Bowtie2 and convert them to BAM format. PGCGROWTHCONDITIONS
Wild type E. coli K-12 (strain BW38038) and BW39452(ΔrpoS) cultures were grown on MOPS glucose minimal medium with 0.2% glucose as sole carbon source at 37°C, pH was initially 7.4,  and the agitation speed was 500 rpm. Culture samples were harvested during logarithmic growth and  following entry into stationary phase for the WT and rpoS mutant. OD600 measurements were made on a Beckman Coulter DU 800 spectrophotometer. Samples were harvested directly into ice-cold RNAlater at a 1:1 dilution to protect RNA from degradation and cells then were pelleted by centrifugation at 8000rpm for 10 minutes. Cell pellets were stored at -80°C in an equal volume of RNAlater prior to RNA extraction. PGCGROWTHCONDITIONS
WT_glucose_log_TEX PGCGROWTHCONDITIONS
All samples were extracted using the hot phenol extraction with DNA digestion, following standard protocol PGCGROWTHCONDITIONS
BigWIG files were viewed and annotated using Jbrowse and Integrated Genome Viewer. PGCGROWTHCONDITIONS
cDNA libraries were constructed at Vertis in Germany using a ligation based stratagey for Illumina whole transcriptome sequencing. Total RNA (DNase I digested) was fragmented by RNase III. RNA samples labeled as TEX were also subsequently digested with Terminator Exonuclease (TEX). Pyrophosphate groups were removed from the 5′ terminus using tobacco acid pyrophosphatase (TAP), and an RNA adapter was ligated to the 5′ end of the RNA. First-strand synthesis was performed using standard Illumina protocols. PGCGROWTHCONDITIONS
Cell culture PGCGROWTHCONDITIONS
Escherichia coli BW38028 PGCGROWTHCONDITIONS
For alignment of the reads contained within the fastq files to the E. coli MG1655 reference genome (RefSeq NC_U00096.3), the short read alignment tool Bowtie2 was utilized under default settings.  Bowtie parameters were set to include only perfect matches and map once reads that map to more than one genome location, i.e., uniquely mapped reads are retained. The output Bowtie2 was a SAM files for each sample. PGCGROWTHCONDITIONS
Genome_build: Reference genome for E. coli MG1655 (RefSeq NC_000913.3). PGCGROWTHCONDITIONS
genotype: wt PGCGROWTHCONDITIONS
growth phase: 30 min post stationary PGCGROWTHCONDITIONS
Prior to total RNA extraction harvested bacterial cells were stored at -80.0°C in an equal volume of RNAlater. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample type: no RNA treatment PGCGROWTHCONDITIONS
Sequence data was processed by conversion of the sample alignment (BAM) files to strand-specific base count (BigWIG) files. To accomplish this an in-house script was created to extract strand-specific base count data from BAM files (outputs are positive and negative strand BigWIG files). PGCGROWTHCONDITIONS
strain: BW38028 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWIG files are provided showing uniquely mapped sequence reads. PGCGROWTHCONDITIONS
The data output from the Illumina Hiseq System was obtained directly from Vertis PGCGROWTHCONDITIONS
treatment: Carbon starvation PGCGROWTHCONDITIONS
Used SAMTOOLS (Li, et al., PMID 1950593) to sort and index the SAM files obtained from Bowtie2 and convert them to BAM format. PGCGROWTHCONDITIONS
Wild type E. coli K-12 (strain BW38038) and BW39452(ΔrpoS) cultures were grown on MOPS glucose minimal medium with 0.2% glucose as sole carbon source at 37°C, pH was initially 7.4,  and the agitation speed was 500 rpm. Culture samples were harvested during logarithmic growth and  following entry into stationary phase for the WT and rpoS mutant. OD600 measurements were made on a Beckman Coulter DU 800 spectrophotometer. Samples were harvested directly into ice-cold RNAlater at a 1:1 dilution to protect RNA from degradation and cells then were pelleted by centrifugation at 8000rpm for 10 minutes. Cell pellets were stored at -80°C in an equal volume of RNAlater prior to RNA extraction. PGCGROWTHCONDITIONS
WT_glucose_stat_TEX PGCGROWTHCONDITIONS
All samples were extracted using the hot phenol extraction with DNA digestion, following standard protocol PGCGROWTHCONDITIONS
BigWIG files were viewed and annotated using Jbrowse and Integrated Genome Viewer. PGCGROWTHCONDITIONS
cDNA libraries were constructed at Vertis in Germany using a ligation based stratagey for Illumina whole transcriptome sequencing. Total RNA (DNase I digested) was fragmented by RNase III. RNA samples labeled as TEX were also subsequently digested with Terminator Exonuclease (TEX). Pyrophosphate groups were removed from the 5′ terminus using tobacco acid pyrophosphatase (TAP), and an RNA adapter was ligated to the 5′ end of the RNA. First-strand synthesis was performed using standard Illumina protocols. PGCGROWTHCONDITIONS
Cell culture PGCGROWTHCONDITIONS
Escherichia coli BW38028 PGCGROWTHCONDITIONS
For alignment of the reads contained within the fastq files to the E. coli MG1655 reference genome (RefSeq NC_U00096.3), the short read alignment tool Bowtie2 was utilized under default settings.  Bowtie parameters were set to include only perfect matches and map once reads that map to more than one genome location, i.e., uniquely mapped reads are retained. The output Bowtie2 was a SAM files for each sample. PGCGROWTHCONDITIONS
Genome_build: Reference genome for E. coli MG1655 (RefSeq NC_000913.3). PGCGROWTHCONDITIONS
genotype: wt PGCGROWTHCONDITIONS
growth phase: 30 min post stationary PGCGROWTHCONDITIONS
Prior to total RNA extraction harvested bacterial cells were stored at -80.0°C in an equal volume of RNAlater. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample type: no RNA treatment PGCGROWTHCONDITIONS
Sequence data was processed by conversion of the sample alignment (BAM) files to strand-specific base count (BigWIG) files. To accomplish this an in-house script was created to extract strand-specific base count data from BAM files (outputs are positive and negative strand BigWIG files). PGCGROWTHCONDITIONS
strain: BW38028 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWIG files are provided showing uniquely mapped sequence reads. PGCGROWTHCONDITIONS
The data output from the Illumina Hiseq System was obtained directly from Vertis PGCGROWTHCONDITIONS
treatment: Nitrogen starvation PGCGROWTHCONDITIONS
Used SAMTOOLS (Li, et al., PMID 1950593) to sort and index the SAM files obtained from Bowtie2 and convert them to BAM format. PGCGROWTHCONDITIONS
Wild type E. coli K-12 (strain BW38038) and BW39452(ΔrpoS) cultures were grown on MOPS glucose minimal medium with 0.2% glucose as sole carbon source at 37°C, pH was initially 7.4,  and the agitation speed was 500 rpm. Culture samples were harvested during logarithmic growth and  following entry into stationary phase for the WT and rpoS mutant. OD600 measurements were made on a Beckman Coulter DU 800 spectrophotometer. Samples were harvested directly into ice-cold RNAlater at a 1:1 dilution to protect RNA from degradation and cells then were pelleted by centrifugation at 8000rpm for 10 minutes. Cell pellets were stored at -80°C in an equal volume of RNAlater prior to RNA extraction. PGCGROWTHCONDITIONS
WT_N_strv_TEX PGCGROWTHCONDITIONS
All samples were extracted using the hot phenol extraction with DNA digestion, following standard protocol PGCGROWTHCONDITIONS
BigWIG files were viewed and annotated using Jbrowse and Integrated Genome Viewer. PGCGROWTHCONDITIONS
cDNA libraries were constructed at Vertis in Germany using a ligation based stratagey for Illumina whole transcriptome sequencing. Total RNA (DNase I digested) was fragmented by RNase III. RNA samples labeled as TEX were also subsequently digested with Terminator Exonuclease (TEX). Pyrophosphate groups were removed from the 5′ terminus using tobacco acid pyrophosphatase (TAP), and an RNA adapter was ligated to the 5′ end of the RNA. First-strand synthesis was performed using standard Illumina protocols. PGCGROWTHCONDITIONS
Cell culture PGCGROWTHCONDITIONS
Escherichia coli BW38028 PGCGROWTHCONDITIONS
For alignment of the reads contained within the fastq files to the E. coli MG1655 reference genome (RefSeq NC_U00096.3), the short read alignment tool Bowtie2 was utilized under default settings.  Bowtie parameters were set to include only perfect matches and map once reads that map to more than one genome location, i.e., uniquely mapped reads are retained. The output Bowtie2 was a SAM files for each sample. PGCGROWTHCONDITIONS
Genome_build: Reference genome for E. coli MG1655 (RefSeq NC_000913.3). PGCGROWTHCONDITIONS
genotype: rpoS PGCGROWTHCONDITIONS
growth phase: 30 min post stationary PGCGROWTHCONDITIONS
Prior to total RNA extraction harvested bacterial cells were stored at -80.0°C in an equal volume of RNAlater. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rpoS_N_strv_TEX PGCGROWTHCONDITIONS
sample type: no RNA treatment PGCGROWTHCONDITIONS
Sequence data was processed by conversion of the sample alignment (BAM) files to strand-specific base count (BigWIG) files. To accomplish this an in-house script was created to extract strand-specific base count data from BAM files (outputs are positive and negative strand BigWIG files). PGCGROWTHCONDITIONS
strain: BW38028 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BigWIG files are provided showing uniquely mapped sequence reads. PGCGROWTHCONDITIONS
The data output from the Illumina Hiseq System was obtained directly from Vertis PGCGROWTHCONDITIONS
treatment: Nitrogen starvation PGCGROWTHCONDITIONS
Used SAMTOOLS (Li, et al., PMID 1950593) to sort and index the SAM files obtained from Bowtie2 and convert them to BAM format. PGCGROWTHCONDITIONS
Wild type E. coli K-12 (strain BW38038) and BW39452(ΔrpoS) cultures were grown on MOPS glucose minimal medium with 0.2% glucose as sole carbon source at 37°C, pH was initially 7.4,  and the agitation speed was 500 rpm. Culture samples were harvested during logarithmic growth and  following entry into stationary phase for the WT and rpoS mutant. OD600 measurements were made on a Beckman Coulter DU 800 spectrophotometer. Samples were harvested directly into ice-cold RNAlater at a 1:1 dilution to protect RNA from degradation and cells then were pelleted by centrifugation at 8000rpm for 10 minutes. Cell pellets were stored at -80°C in an equal volume of RNAlater prior to RNA extraction. PGCGROWTHCONDITIONS
At OD ~0.3, cultures were induced with 1mM IPTG for the appropriate length of time. PGCGROWTHCONDITIONS
Bacteria were grown at 30C with shaking (~200 rpm) in fully supplemented MOPS glucose media (Teknova) to OD420 ~0.4. Cultures were split into 4 subcultures, and grown to OD ~0.3. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E coli genome were converted to wiggle files. The position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011). 200 ml of cell culture was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C. PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
media: fully supplemented MOPS glucose media PGCGROWTHCONDITIONS
molecule subtype: mRNA PGCGROWTHCONDITIONS
mRNA-seq in rich defined media PGCGROWTHCONDITIONS
mRNA-seq Vector t0 PGCGROWTHCONDITIONS
Ribosome protected and total mRNA fragments were size selected via gel purification. Fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More details at MS Guo, TB Updegrove, et al, Genes Dev. (2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E coli genome using parameters -v 1 -m 1 --best. This allows one mismatch and reports only reads that align 1 or fewer times to the genome PGCGROWTHCONDITIONS
At OD ~0.3, cultures were induced with 1mM IPTG for the appropriate length of time. PGCGROWTHCONDITIONS
Bacteria were grown at 30C with shaking (~200 rpm) in fully supplemented MOPS glucose media (Teknova) to OD420 ~0.4. Cultures were split into 4 subcultures, and grown to OD ~0.3. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E coli genome were converted to wiggle files. The position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011). 200 ml of cell culture was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C. PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
media: fully supplemented MOPS glucose media PGCGROWTHCONDITIONS
molecule subtype: mRNA PGCGROWTHCONDITIONS
mRNA-seq in rich defined media PGCGROWTHCONDITIONS
mRNA-seq Vector t20 PGCGROWTHCONDITIONS
Ribosome protected and total mRNA fragments were size selected via gel purification. Fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More details at MS Guo, TB Updegrove, et al, Genes Dev. (2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E coli genome using parameters -v 1 -m 1 --best. This allows one mismatch and reports only reads that align 1 or fewer times to the genome PGCGROWTHCONDITIONS
At OD ~0.3, cultures were induced with 1mM IPTG for the appropriate length of time. PGCGROWTHCONDITIONS
Bacteria were grown at 30C with shaking (~200 rpm) in fully supplemented MOPS glucose media (Teknova) to OD420 ~0.4. Cultures were split into 4 subcultures, and grown to OD ~0.3. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E coli genome were converted to wiggle files. The position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011). 200 ml of cell culture was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C. PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
media: fully supplemented MOPS glucose media PGCGROWTHCONDITIONS
molecule subtype: mRNA PGCGROWTHCONDITIONS
mRNA-seq in rich defined media PGCGROWTHCONDITIONS
mRNA-seq MicL t0 PGCGROWTHCONDITIONS
Ribosome protected and total mRNA fragments were size selected via gel purification. Fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More details at MS Guo, TB Updegrove, et al, Genes Dev. (2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E coli genome using parameters -v 1 -m 1 --best. This allows one mismatch and reports only reads that align 1 or fewer times to the genome PGCGROWTHCONDITIONS
At OD ~0.3, cultures were induced with 1mM IPTG for the appropriate length of time. PGCGROWTHCONDITIONS
Bacteria were grown at 30C with shaking (~200 rpm) in fully supplemented MOPS glucose media (Teknova) to OD420 ~0.4. Cultures were split into 4 subcultures, and grown to OD ~0.3. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E coli genome were converted to wiggle files. The position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011). 200 ml of cell culture was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C. PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
media: fully supplemented MOPS glucose media PGCGROWTHCONDITIONS
molecule subtype: mRNA PGCGROWTHCONDITIONS
mRNA-seq in rich defined media PGCGROWTHCONDITIONS
mRNA-seq MicL t20 PGCGROWTHCONDITIONS
Ribosome protected and total mRNA fragments were size selected via gel purification. Fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More details at MS Guo, TB Updegrove, et al, Genes Dev. (2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E coli genome using parameters -v 1 -m 1 --best. This allows one mismatch and reports only reads that align 1 or fewer times to the genome PGCGROWTHCONDITIONS
At OD ~0.3, cultures were induced with 1mM IPTG for the appropriate length of time. PGCGROWTHCONDITIONS
Bacteria were grown at 30C with shaking (~200 rpm) in fully supplemented MOPS glucose media (Teknova) to OD420 ~0.4. Cultures were split into 4 subcultures, and grown to OD ~0.3. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E coli genome were converted to wiggle files. The position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011). 200 ml of cell culture was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C. PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
media: fully supplemented MOPS glucose media PGCGROWTHCONDITIONS
molecule subtype: ribosome protected mRNA PGCGROWTHCONDITIONS
ribosome profiling in rich defined media PGCGROWTHCONDITIONS
ribosome profiling MicL t0 PGCGROWTHCONDITIONS
Ribosome protected and total mRNA fragments were size selected via gel purification. Fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More details at MS Guo, TB Updegrove, et al, Genes Dev. (2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E coli genome using parameters -v 1 -m 1 --best. This allows one mismatch and reports only reads that align 1 or fewer times to the genome PGCGROWTHCONDITIONS
At OD ~0.3, cultures were induced with 1mM IPTG for the appropriate length of time. PGCGROWTHCONDITIONS
Bacteria were grown at 30C with shaking (~200 rpm) in fully supplemented MOPS glucose media (Teknova) to OD420 ~0.4. Cultures were split into 4 subcultures, and grown to OD ~0.3. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E coli genome were converted to wiggle files. The position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011). 200 ml of cell culture was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C. PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
media: fully supplemented MOPS glucose media PGCGROWTHCONDITIONS
molecule subtype: ribosome protected mRNA PGCGROWTHCONDITIONS
ribosome profiling in rich defined media PGCGROWTHCONDITIONS
ribosome profiling MicL t20 PGCGROWTHCONDITIONS
Ribosome protected and total mRNA fragments were size selected via gel purification. Fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More details at MS Guo, TB Updegrove, et al, Genes Dev. (2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E coli genome using parameters -v 1 -m 1 --best. This allows one mismatch and reports only reads that align 1 or fewer times to the genome PGCGROWTHCONDITIONS
At OD ~0.3, cultures were induced with 1mM IPTG for the appropriate length of time. PGCGROWTHCONDITIONS
bacteria PGCGROWTHCONDITIONS
Bacteria were grown at 30C with shaking (~200 rpm) in fully supplemented MOPS glucose media (Teknova) to OD420 ~0.4. Cultures were split into 4 subcultures, and grown to OD ~0.3. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E coli genome were converted to wiggle files. The position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011). 200 ml of cell culture was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C. PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
media: fully supplemented MOPS glucose media PGCGROWTHCONDITIONS
mRNA-seq WT t4 PGCGROWTHCONDITIONS
plasmid: empty vector PGCGROWTHCONDITIONS
Ribosome protected and total mRNA fragments were size selected via gel purification. Fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More details at MS Guo, TB Updegrove, et al, Genes Dev. (2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E coli genome using parameters -v 1 -m 1 --best. This allows one mismatch and reports only reads that align 1 or fewer times to the genome PGCGROWTHCONDITIONS
At OD ~0.3, cultures were induced with 1mM IPTG for the appropriate length of time. PGCGROWTHCONDITIONS
bacteria PGCGROWTHCONDITIONS
Bacteria were grown at 30C with shaking (~200 rpm) in fully supplemented MOPS glucose media (Teknova) to OD420 ~0.4. Cultures were split into 4 subcultures, and grown to OD ~0.3. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E coli genome were converted to wiggle files. The position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011). 200 ml of cell culture was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C. PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
media: fully supplemented MOPS glucose media PGCGROWTHCONDITIONS
mRNA-seq WT t10 PGCGROWTHCONDITIONS
plasmid: empty vector PGCGROWTHCONDITIONS
Ribosome protected and total mRNA fragments were size selected via gel purification. Fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More details at MS Guo, TB Updegrove, et al, Genes Dev. (2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E coli genome using parameters -v 1 -m 1 --best. This allows one mismatch and reports only reads that align 1 or fewer times to the genome PGCGROWTHCONDITIONS
At OD ~0.3, cultures were induced with 1mM IPTG for the appropriate length of time. PGCGROWTHCONDITIONS
bacteria PGCGROWTHCONDITIONS
Bacteria were grown at 30C with shaking (~200 rpm) in fully supplemented MOPS glucose media (Teknova) to OD420 ~0.4. Cultures were split into 4 subcultures, and grown to OD ~0.3. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E coli genome were converted to wiggle files. The position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011). 200 ml of cell culture was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C. PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
media: fully supplemented MOPS glucose media PGCGROWTHCONDITIONS
mRNA-seq MicL-S t0 PGCGROWTHCONDITIONS
plasmid: pMicL-S PGCGROWTHCONDITIONS
Ribosome protected and total mRNA fragments were size selected via gel purification. Fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More details at MS Guo, TB Updegrove, et al, Genes Dev. (2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E coli genome using parameters -v 1 -m 1 --best. This allows one mismatch and reports only reads that align 1 or fewer times to the genome PGCGROWTHCONDITIONS
At OD ~0.3, cultures were induced with 1mM IPTG for the appropriate length of time. PGCGROWTHCONDITIONS
bacteria PGCGROWTHCONDITIONS
Bacteria were grown at 30C with shaking (~200 rpm) in fully supplemented MOPS glucose media (Teknova) to OD420 ~0.4. Cultures were split into 4 subcultures, and grown to OD ~0.3. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E coli genome were converted to wiggle files. The position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011). 200 ml of cell culture was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C. PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
media: fully supplemented MOPS glucose media PGCGROWTHCONDITIONS
mRNA-seq MicL-S t4 PGCGROWTHCONDITIONS
plasmid: pMicL-S PGCGROWTHCONDITIONS
Ribosome protected and total mRNA fragments were size selected via gel purification. Fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More details at MS Guo, TB Updegrove, et al, Genes Dev. (2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E coli genome using parameters -v 1 -m 1 --best. This allows one mismatch and reports only reads that align 1 or fewer times to the genome PGCGROWTHCONDITIONS
At OD ~0.3, cultures were induced with 1mM IPTG for the appropriate length of time. PGCGROWTHCONDITIONS
bacteria PGCGROWTHCONDITIONS
Bacteria were grown at 30C with shaking (~200 rpm) in fully supplemented MOPS glucose media (Teknova) to OD420 ~0.4. Cultures were split into 4 subcultures, and grown to OD ~0.3. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E coli genome were converted to wiggle files. The position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011). 200 ml of cell culture was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C. PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
media: fully supplemented MOPS glucose media PGCGROWTHCONDITIONS
mRNA-seq MicL-S t10 PGCGROWTHCONDITIONS
plasmid: pMicL-S PGCGROWTHCONDITIONS
Ribosome protected and total mRNA fragments were size selected via gel purification. Fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More details at MS Guo, TB Updegrove, et al, Genes Dev. (2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E coli genome using parameters -v 1 -m 1 --best. This allows one mismatch and reports only reads that align 1 or fewer times to the genome PGCGROWTHCONDITIONS
At OD ~0.3, cultures were induced with 1mM IPTG for the appropriate length of time. PGCGROWTHCONDITIONS
bacteria PGCGROWTHCONDITIONS
Bacteria were grown at 30C with shaking (~200 rpm) in fully supplemented MOPS glucose media (Teknova) to OD420 ~0.4. Cultures were split into 4 subcultures, and grown to OD ~0.3. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E coli genome were converted to wiggle files. The position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011). 200 ml of cell culture was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C. PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
media: fully supplemented MOPS glucose media PGCGROWTHCONDITIONS
mRNA-seq MicL-S t20 PGCGROWTHCONDITIONS
plasmid: pMicL-S PGCGROWTHCONDITIONS
Ribosome protected and total mRNA fragments were size selected via gel purification. Fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More details at MS Guo, TB Updegrove, et al, Genes Dev. (2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E coli genome using parameters -v 1 -m 1 --best. This allows one mismatch and reports only reads that align 1 or fewer times to the genome PGCGROWTHCONDITIONS
At OD ~0.3, cultures were induced with 1mM IPTG for the appropriate length of time. PGCGROWTHCONDITIONS
bacteria PGCGROWTHCONDITIONS
Bacteria were grown at 30C with shaking (~200 rpm) in fully supplemented MOPS glucose media (Teknova) to OD420 ~0.4. Cultures were split into 4 subcultures, and grown to OD ~0.3. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E coli genome were converted to wiggle files. The position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011). 200 ml of cell culture was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C. PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
media: fully supplemented MOPS glucose media PGCGROWTHCONDITIONS
mRNA-seq MicL t4 PGCGROWTHCONDITIONS
plasmid: pMicL PGCGROWTHCONDITIONS
Ribosome protected and total mRNA fragments were size selected via gel purification. Fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More details at MS Guo, TB Updegrove, et al, Genes Dev. (2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E coli genome using parameters -v 1 -m 1 --best. This allows one mismatch and reports only reads that align 1 or fewer times to the genome PGCGROWTHCONDITIONS
At OD ~0.3, cultures were induced with 1mM IPTG for the appropriate length of time. PGCGROWTHCONDITIONS
bacteria PGCGROWTHCONDITIONS
Bacteria were grown at 30C with shaking (~200 rpm) in fully supplemented MOPS glucose media (Teknova) to OD420 ~0.4. Cultures were split into 4 subcultures, and grown to OD ~0.3. PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E coli genome were converted to wiggle files. The position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011). 200 ml of cell culture was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C. PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
media: fully supplemented MOPS glucose media PGCGROWTHCONDITIONS
mRNA-seq MicL t10 PGCGROWTHCONDITIONS
plasmid: pMicL PGCGROWTHCONDITIONS
Ribosome protected and total mRNA fragments were size selected via gel purification. Fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More details at MS Guo, TB Updegrove, et al, Genes Dev. (2014). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E coli genome using parameters -v 1 -m 1 --best. This allows one mismatch and reports only reads that align 1 or fewer times to the genome PGCGROWTHCONDITIONS
Basecalling was done on the sequencers using the sequencer's Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format. PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C. PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FASTQ formatted sequence files from strand-specific Illumina RNA-Seq reads were aligned to the GLBRCE1 reference genome NC_000913 using Bowtie version 0.12.7(Langmead et al., 2009) with '--nofw' strand-specific parameter and maximal distance between the paired reads of 1000 bp. NOTE: Genome NC_000913 (ASM584v2) represents the parental strain.  The strain used in our study was modified from the parental strain by replacing gene pflB with an insertion that contained 3 different genes. PGCGROWTHCONDITIONS
Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2 PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth phase: Exp PGCGROWTHCONDITIONS
medium: SynH PGCGROWTHCONDITIONS
Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C PGCGROWTHCONDITIONS
strain: GLBRCE1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded. PGCGROWTHCONDITIONS
SynH_Exp_CBYS PGCGROWTHCONDITIONS
Total RNA (2ug) was subjected to rRNA depletion using Ribozero rRNA removal kit – Bacteria (Epicenter, illumina). rRNA-depleted RNA was purified using Ampure XP beads. Purified RNA was then fragmented using RNA Fragmentation Reagents (Ambion) at 70C for 2mins, targeting fragments ranging from 200-300bp. Fragmented RNA was then purified using Ampure XP beads (Agencourt). Reverse transcription was performed using SuperScript II Reverse Transcription (Invitrogen) with an initial annealing of random hexamers (Fermentas) at 65C for 5mins, follow by an incubation of 42C for 50mins and an inactivation step at 70C for 10mins. cDNA was then purified with Ampure XP beads. This was followed by second strand synthesis using dNTP mix where dTTP is replaced by dUTP. Reaction was performed at 16C for 1h. Double stranded cDNA fragments were purified and selected for targeted fragments (200-300bp) using Ampure XP beads. The dscDNA were then blunt-ended, the 3' ends were adenylated with a single A, and ligated with library adapters using Kapa Library Amplification Kit (Kapa Biosystems). Adapter-ligated DNA was purified using Ampure XP beads. Digestion of dUTP was then performed using AmpErase UNG (Applied Biosystems) to remove second strand cDNA. Digested cDNA was again cleaned up with Ampure SPRI beads. This was followed by amplification by 10 cycles of PCR using Kapa Library Amplification Kit (Kapa Biosystems). The final library was cleaned up with Ampure SPRI beads. Sequencing was done on the Illumina HiSeq platform generating paired end reads of 100bp each. Note: Target fragments here refers to the insert only, that is the cDNA.  The actual size we use in selection will be larger, typically the target fragment size + 125bp adaptors (~300-450bp). PGCGROWTHCONDITIONS
Basecalling was done on the sequencers using the sequencer's Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format. PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C. PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FASTQ formatted sequence files from strand-specific Illumina RNA-Seq reads were aligned to the GLBRCE1 reference genome NC_000913 using Bowtie version 0.12.7(Langmead et al., 2009) with '--nofw' strand-specific parameter and maximal distance between the paired reads of 1000 bp. NOTE: Genome NC_000913 (ASM584v2) represents the parental strain.  The strain used in our study was modified from the parental strain by replacing gene pflB with an insertion that contained 3 different genes. PGCGROWTHCONDITIONS
Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2 PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth phase: Exp PGCGROWTHCONDITIONS
medium: SynH PGCGROWTHCONDITIONS
Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C PGCGROWTHCONDITIONS
strain: GLBRCE1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded. PGCGROWTHCONDITIONS
SynH_Exp_BXHU PGCGROWTHCONDITIONS
Total RNA (2ug) was subjected to rRNA depletion using Ribozero rRNA removal kit – Bacteria (Epicenter, illumina). rRNA-depleted RNA was purified using Ampure XP beads. Purified RNA was then fragmented using RNA Fragmentation Reagents (Ambion) at 70C for 2mins, targeting fragments ranging from 200-300bp. Fragmented RNA was then purified using Ampure XP beads (Agencourt). Reverse transcription was performed using SuperScript II Reverse Transcription (Invitrogen) with an initial annealing of random hexamers (Fermentas) at 65C for 5mins, follow by an incubation of 42C for 50mins and an inactivation step at 70C for 10mins. cDNA was then purified with Ampure XP beads. This was followed by second strand synthesis using dNTP mix where dTTP is replaced by dUTP. Reaction was performed at 16C for 1h. Double stranded cDNA fragments were purified and selected for targeted fragments (200-300bp) using Ampure XP beads. The dscDNA were then blunt-ended, the 3' ends were adenylated with a single A, and ligated with library adapters using Kapa Library Amplification Kit (Kapa Biosystems). Adapter-ligated DNA was purified using Ampure XP beads. Digestion of dUTP was then performed using AmpErase UNG (Applied Biosystems) to remove second strand cDNA. Digested cDNA was again cleaned up with Ampure SPRI beads. This was followed by amplification by 10 cycles of PCR using Kapa Library Amplification Kit (Kapa Biosystems). The final library was cleaned up with Ampure SPRI beads. Sequencing was done on the Illumina HiSeq platform generating paired end reads of 100bp each. Note: Target fragments here refers to the insert only, that is the cDNA.  The actual size we use in selection will be larger, typically the target fragment size + 125bp adaptors (~300-450bp). PGCGROWTHCONDITIONS
Basecalling was done on the sequencers using the sequencer's Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format. PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C. PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FASTQ formatted sequence files from strand-specific Illumina RNA-Seq reads were aligned to the GLBRCE1 reference genome NC_000913 using Bowtie version 0.12.7(Langmead et al., 2009) with '--nofw' strand-specific parameter and maximal distance between the paired reads of 1000 bp. NOTE: Genome NC_000913 (ASM584v2) represents the parental strain.  The strain used in our study was modified from the parental strain by replacing gene pflB with an insertion that contained 3 different genes. PGCGROWTHCONDITIONS
Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2 PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth phase: Exp PGCGROWTHCONDITIONS
medium: SynH_LT PGCGROWTHCONDITIONS
Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C PGCGROWTHCONDITIONS
strain: GLBRCE1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded. PGCGROWTHCONDITIONS
SynH_LT_Exp_CCOG PGCGROWTHCONDITIONS
Total RNA (2ug) was subjected to rRNA depletion using Ribozero rRNA removal kit – Bacteria (Epicenter, illumina). rRNA-depleted RNA was purified using Ampure XP beads. Purified RNA was then fragmented using RNA Fragmentation Reagents (Ambion) at 70C for 2mins, targeting fragments ranging from 200-300bp. Fragmented RNA was then purified using Ampure XP beads (Agencourt). Reverse transcription was performed using SuperScript II Reverse Transcription (Invitrogen) with an initial annealing of random hexamers (Fermentas) at 65C for 5mins, follow by an incubation of 42C for 50mins and an inactivation step at 70C for 10mins. cDNA was then purified with Ampure XP beads. This was followed by second strand synthesis using dNTP mix where dTTP is replaced by dUTP. Reaction was performed at 16C for 1h. Double stranded cDNA fragments were purified and selected for targeted fragments (200-300bp) using Ampure XP beads. The dscDNA were then blunt-ended, the 3' ends were adenylated with a single A, and ligated with library adapters using Kapa Library Amplification Kit (Kapa Biosystems). Adapter-ligated DNA was purified using Ampure XP beads. Digestion of dUTP was then performed using AmpErase UNG (Applied Biosystems) to remove second strand cDNA. Digested cDNA was again cleaned up with Ampure SPRI beads. This was followed by amplification by 10 cycles of PCR using Kapa Library Amplification Kit (Kapa Biosystems). The final library was cleaned up with Ampure SPRI beads. Sequencing was done on the Illumina HiSeq platform generating paired end reads of 100bp each. Note: Target fragments here refers to the insert only, that is the cDNA.  The actual size we use in selection will be larger, typically the target fragment size + 125bp adaptors (~300-450bp). PGCGROWTHCONDITIONS
Basecalling was done on the sequencers using the sequencer's Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format. PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C. PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FASTQ formatted sequence files from strand-specific Illumina RNA-Seq reads were aligned to the GLBRCE1 reference genome NC_000913 using Bowtie version 0.12.7(Langmead et al., 2009) with '--nofw' strand-specific parameter and maximal distance between the paired reads of 1000 bp. NOTE: Genome NC_000913 (ASM584v2) represents the parental strain.  The strain used in our study was modified from the parental strain by replacing gene pflB with an insertion that contained 3 different genes. PGCGROWTHCONDITIONS
Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2 PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth phase: Exp PGCGROWTHCONDITIONS
medium: SynH_LT PGCGROWTHCONDITIONS
Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C PGCGROWTHCONDITIONS
strain: GLBRCE1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded. PGCGROWTHCONDITIONS
SynH_LT_Exp_BXNX PGCGROWTHCONDITIONS
Total RNA (2ug) was subjected to rRNA depletion using Ribozero rRNA removal kit – Bacteria (Epicenter, illumina). rRNA-depleted RNA was purified using Ampure XP beads. Purified RNA was then fragmented using RNA Fragmentation Reagents (Ambion) at 70C for 2mins, targeting fragments ranging from 200-300bp. Fragmented RNA was then purified using Ampure XP beads (Agencourt). Reverse transcription was performed using SuperScript II Reverse Transcription (Invitrogen) with an initial annealing of random hexamers (Fermentas) at 65C for 5mins, follow by an incubation of 42C for 50mins and an inactivation step at 70C for 10mins. cDNA was then purified with Ampure XP beads. This was followed by second strand synthesis using dNTP mix where dTTP is replaced by dUTP. Reaction was performed at 16C for 1h. Double stranded cDNA fragments were purified and selected for targeted fragments (200-300bp) using Ampure XP beads. The dscDNA were then blunt-ended, the 3' ends were adenylated with a single A, and ligated with library adapters using Kapa Library Amplification Kit (Kapa Biosystems). Adapter-ligated DNA was purified using Ampure XP beads. Digestion of dUTP was then performed using AmpErase UNG (Applied Biosystems) to remove second strand cDNA. Digested cDNA was again cleaned up with Ampure SPRI beads. This was followed by amplification by 10 cycles of PCR using Kapa Library Amplification Kit (Kapa Biosystems). The final library was cleaned up with Ampure SPRI beads. Sequencing was done on the Illumina HiSeq platform generating paired end reads of 100bp each. Note: Target fragments here refers to the insert only, that is the cDNA.  The actual size we use in selection will be larger, typically the target fragment size + 125bp adaptors (~300-450bp). PGCGROWTHCONDITIONS
Basecalling was done on the sequencers using the sequencer's Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format. PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C. PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FASTQ formatted sequence files from strand-specific Illumina RNA-Seq reads were aligned to the GLBRCE1 reference genome NC_000913 using Bowtie version 0.12.7(Langmead et al., 2009) with '--nofw' strand-specific parameter and maximal distance between the paired reads of 1000 bp. NOTE: Genome NC_000913 (ASM584v2) represents the parental strain.  The strain used in our study was modified from the parental strain by replacing gene pflB with an insertion that contained 3 different genes. PGCGROWTHCONDITIONS
Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2 PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth phase: Exp PGCGROWTHCONDITIONS
medium: SynH_LT PGCGROWTHCONDITIONS
Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C PGCGROWTHCONDITIONS
strain: GLBRCE1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded. PGCGROWTHCONDITIONS
SynH_LT_Exp_CBYU PGCGROWTHCONDITIONS
Total RNA (2ug) was subjected to rRNA depletion using Ribozero rRNA removal kit – Bacteria (Epicenter, illumina). rRNA-depleted RNA was purified using Ampure XP beads. Purified RNA was then fragmented using RNA Fragmentation Reagents (Ambion) at 70C for 2mins, targeting fragments ranging from 200-300bp. Fragmented RNA was then purified using Ampure XP beads (Agencourt). Reverse transcription was performed using SuperScript II Reverse Transcription (Invitrogen) with an initial annealing of random hexamers (Fermentas) at 65C for 5mins, follow by an incubation of 42C for 50mins and an inactivation step at 70C for 10mins. cDNA was then purified with Ampure XP beads. This was followed by second strand synthesis using dNTP mix where dTTP is replaced by dUTP. Reaction was performed at 16C for 1h. Double stranded cDNA fragments were purified and selected for targeted fragments (200-300bp) using Ampure XP beads. The dscDNA were then blunt-ended, the 3' ends were adenylated with a single A, and ligated with library adapters using Kapa Library Amplification Kit (Kapa Biosystems). Adapter-ligated DNA was purified using Ampure XP beads. Digestion of dUTP was then performed using AmpErase UNG (Applied Biosystems) to remove second strand cDNA. Digested cDNA was again cleaned up with Ampure SPRI beads. This was followed by amplification by 10 cycles of PCR using Kapa Library Amplification Kit (Kapa Biosystems). The final library was cleaned up with Ampure SPRI beads. Sequencing was done on the Illumina HiSeq platform generating paired end reads of 100bp each. Note: Target fragments here refers to the insert only, that is the cDNA.  The actual size we use in selection will be larger, typically the target fragment size + 125bp adaptors (~300-450bp). PGCGROWTHCONDITIONS
ACSH_Exp_CNFT PGCGROWTHCONDITIONS
Basecalling was done on the sequencers using the sequencer's Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format. PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C. PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FASTQ formatted sequence files from strand-specific Illumina RNA-Seq reads were aligned to the GLBRCE1 reference genome NC_000913 using Bowtie version 0.12.7(Langmead et al., 2009) with '--nofw' strand-specific parameter and maximal distance between the paired reads of 1000 bp. NOTE: Genome NC_000913 (ASM584v2) represents the parental strain.  The strain used in our study was modified from the parental strain by replacing gene pflB with an insertion that contained 3 different genes. PGCGROWTHCONDITIONS
Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2 PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth phase: Exp PGCGROWTHCONDITIONS
medium: ACSH PGCGROWTHCONDITIONS
Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C PGCGROWTHCONDITIONS
strain: GLBRCE1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded. PGCGROWTHCONDITIONS
Total RNA (2ug) was subjected to rRNA depletion using Ribozero rRNA removal kit – Bacteria (Epicenter, illumina). rRNA-depleted RNA was purified using Ampure XP beads. Purified RNA was then fragmented using RNA Fragmentation Reagents (Ambion) at 70C for 2mins, targeting fragments ranging from 200-300bp. Fragmented RNA was then purified using Ampure XP beads (Agencourt). Reverse transcription was performed using SuperScript II Reverse Transcription (Invitrogen) with an initial annealing of random hexamers (Fermentas) at 65C for 5mins, follow by an incubation of 42C for 50mins and an inactivation step at 70C for 10mins. cDNA was then purified with Ampure XP beads. This was followed by second strand synthesis using dNTP mix where dTTP is replaced by dUTP. Reaction was performed at 16C for 1h. Double stranded cDNA fragments were purified and selected for targeted fragments (200-300bp) using Ampure XP beads. The dscDNA were then blunt-ended, the 3' ends were adenylated with a single A, and ligated with library adapters using Kapa Library Amplification Kit (Kapa Biosystems). Adapter-ligated DNA was purified using Ampure XP beads. Digestion of dUTP was then performed using AmpErase UNG (Applied Biosystems) to remove second strand cDNA. Digested cDNA was again cleaned up with Ampure SPRI beads. This was followed by amplification by 10 cycles of PCR using Kapa Library Amplification Kit (Kapa Biosystems). The final library was cleaned up with Ampure SPRI beads. Sequencing was done on the Illumina HiSeq platform generating paired end reads of 100bp each. Note: Target fragments here refers to the insert only, that is the cDNA.  The actual size we use in selection will be larger, typically the target fragment size + 125bp adaptors (~300-450bp). PGCGROWTHCONDITIONS
ACSH_Exp_CIYS PGCGROWTHCONDITIONS
Basecalling was done on the sequencers using the sequencer's Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format. PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C. PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FASTQ formatted sequence files from strand-specific Illumina RNA-Seq reads were aligned to the GLBRCE1 reference genome NC_000913 using Bowtie version 0.12.7(Langmead et al., 2009) with '--nofw' strand-specific parameter and maximal distance between the paired reads of 1000 bp. NOTE: Genome NC_000913 (ASM584v2) represents the parental strain.  The strain used in our study was modified from the parental strain by replacing gene pflB with an insertion that contained 3 different genes. PGCGROWTHCONDITIONS
Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2 PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth phase: Exp PGCGROWTHCONDITIONS
medium: ACSH PGCGROWTHCONDITIONS
Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C PGCGROWTHCONDITIONS
strain: GLBRCE1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded. PGCGROWTHCONDITIONS
Total RNA (2ug) was subjected to rRNA depletion using Ribozero rRNA removal kit – Bacteria (Epicenter, illumina). rRNA-depleted RNA was purified using Ampure XP beads. Purified RNA was then fragmented using RNA Fragmentation Reagents (Ambion) at 70C for 2mins, targeting fragments ranging from 200-300bp. Fragmented RNA was then purified using Ampure XP beads (Agencourt). Reverse transcription was performed using SuperScript II Reverse Transcription (Invitrogen) with an initial annealing of random hexamers (Fermentas) at 65C for 5mins, follow by an incubation of 42C for 50mins and an inactivation step at 70C for 10mins. cDNA was then purified with Ampure XP beads. This was followed by second strand synthesis using dNTP mix where dTTP is replaced by dUTP. Reaction was performed at 16C for 1h. Double stranded cDNA fragments were purified and selected for targeted fragments (200-300bp) using Ampure XP beads. The dscDNA were then blunt-ended, the 3' ends were adenylated with a single A, and ligated with library adapters using Kapa Library Amplification Kit (Kapa Biosystems). Adapter-ligated DNA was purified using Ampure XP beads. Digestion of dUTP was then performed using AmpErase UNG (Applied Biosystems) to remove second strand cDNA. Digested cDNA was again cleaned up with Ampure SPRI beads. This was followed by amplification by 10 cycles of PCR using Kapa Library Amplification Kit (Kapa Biosystems). The final library was cleaned up with Ampure SPRI beads. Sequencing was done on the Illumina HiSeq platform generating paired end reads of 100bp each. Note: Target fragments here refers to the insert only, that is the cDNA.  The actual size we use in selection will be larger, typically the target fragment size + 125bp adaptors (~300-450bp). PGCGROWTHCONDITIONS
Basecalling was done on the sequencers using the sequencer's Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format. PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C. PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FASTQ formatted sequence files from strand-specific Illumina RNA-Seq reads were aligned to the GLBRCE1 reference genome NC_000913 using Bowtie version 0.12.7(Langmead et al., 2009) with '--nofw' strand-specific parameter and maximal distance between the paired reads of 1000 bp. NOTE: Genome NC_000913 (ASM584v2) represents the parental strain.  The strain used in our study was modified from the parental strain by replacing gene pflB with an insertion that contained 3 different genes. PGCGROWTHCONDITIONS
Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2 PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth phase: Trans PGCGROWTHCONDITIONS
medium: SynH PGCGROWTHCONDITIONS
Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C PGCGROWTHCONDITIONS
strain: GLBRCE1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded. PGCGROWTHCONDITIONS
SynH_Trans_CUNZ PGCGROWTHCONDITIONS
Total RNA (2ug) was subjected to rRNA depletion using Ribozero rRNA removal kit – Bacteria (Epicenter, illumina). rRNA-depleted RNA was purified using Ampure XP beads. Purified RNA was then fragmented using RNA Fragmentation Reagents (Ambion) at 70C for 2mins, targeting fragments ranging from 200-300bp. Fragmented RNA was then purified using Ampure XP beads (Agencourt). Reverse transcription was performed using SuperScript II Reverse Transcription (Invitrogen) with an initial annealing of random hexamers (Fermentas) at 65C for 5mins, follow by an incubation of 42C for 50mins and an inactivation step at 70C for 10mins. cDNA was then purified with Ampure XP beads. This was followed by second strand synthesis using dNTP mix where dTTP is replaced by dUTP. Reaction was performed at 16C for 1h. Double stranded cDNA fragments were purified and selected for targeted fragments (200-300bp) using Ampure XP beads. The dscDNA were then blunt-ended, the 3' ends were adenylated with a single A, and ligated with library adapters using Kapa Library Amplification Kit (Kapa Biosystems). Adapter-ligated DNA was purified using Ampure XP beads. Digestion of dUTP was then performed using AmpErase UNG (Applied Biosystems) to remove second strand cDNA. Digested cDNA was again cleaned up with Ampure SPRI beads. This was followed by amplification by 10 cycles of PCR using Kapa Library Amplification Kit (Kapa Biosystems). The final library was cleaned up with Ampure SPRI beads. Sequencing was done on the Illumina HiSeq platform generating paired end reads of 100bp each. Note: Target fragments here refers to the insert only, that is the cDNA.  The actual size we use in selection will be larger, typically the target fragment size + 125bp adaptors (~300-450bp). PGCGROWTHCONDITIONS
Basecalling was done on the sequencers using the sequencer's Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format. PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C. PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FASTQ formatted sequence files from strand-specific Illumina RNA-Seq reads were aligned to the GLBRCE1 reference genome NC_000913 using Bowtie version 0.12.7(Langmead et al., 2009) with '--nofw' strand-specific parameter and maximal distance between the paired reads of 1000 bp. NOTE: Genome NC_000913 (ASM584v2) represents the parental strain.  The strain used in our study was modified from the parental strain by replacing gene pflB with an insertion that contained 3 different genes. PGCGROWTHCONDITIONS
Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2 PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth phase: Trans PGCGROWTHCONDITIONS
medium: SynH PGCGROWTHCONDITIONS
Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C PGCGROWTHCONDITIONS
strain: GLBRCE1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded. PGCGROWTHCONDITIONS
SynH_Trans_CUOB PGCGROWTHCONDITIONS
Total RNA (2ug) was subjected to rRNA depletion using Ribozero rRNA removal kit – Bacteria (Epicenter, illumina). rRNA-depleted RNA was purified using Ampure XP beads. Purified RNA was then fragmented using RNA Fragmentation Reagents (Ambion) at 70C for 2mins, targeting fragments ranging from 200-300bp. Fragmented RNA was then purified using Ampure XP beads (Agencourt). Reverse transcription was performed using SuperScript II Reverse Transcription (Invitrogen) with an initial annealing of random hexamers (Fermentas) at 65C for 5mins, follow by an incubation of 42C for 50mins and an inactivation step at 70C for 10mins. cDNA was then purified with Ampure XP beads. This was followed by second strand synthesis using dNTP mix where dTTP is replaced by dUTP. Reaction was performed at 16C for 1h. Double stranded cDNA fragments were purified and selected for targeted fragments (200-300bp) using Ampure XP beads. The dscDNA were then blunt-ended, the 3' ends were adenylated with a single A, and ligated with library adapters using Kapa Library Amplification Kit (Kapa Biosystems). Adapter-ligated DNA was purified using Ampure XP beads. Digestion of dUTP was then performed using AmpErase UNG (Applied Biosystems) to remove second strand cDNA. Digested cDNA was again cleaned up with Ampure SPRI beads. This was followed by amplification by 10 cycles of PCR using Kapa Library Amplification Kit (Kapa Biosystems). The final library was cleaned up with Ampure SPRI beads. Sequencing was done on the Illumina HiSeq platform generating paired end reads of 100bp each. Note: Target fragments here refers to the insert only, that is the cDNA.  The actual size we use in selection will be larger, typically the target fragment size + 125bp adaptors (~300-450bp). PGCGROWTHCONDITIONS
Basecalling was done on the sequencers using the sequencer's Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format. PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C. PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FASTQ formatted sequence files from strand-specific Illumina RNA-Seq reads were aligned to the GLBRCE1 reference genome NC_000913 using Bowtie version 0.12.7(Langmead et al., 2009) with '--nofw' strand-specific parameter and maximal distance between the paired reads of 1000 bp. NOTE: Genome NC_000913 (ASM584v2) represents the parental strain.  The strain used in our study was modified from the parental strain by replacing gene pflB with an insertion that contained 3 different genes. PGCGROWTHCONDITIONS
Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2 PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth phase: Trans PGCGROWTHCONDITIONS
medium: SynH_LT PGCGROWTHCONDITIONS
Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C PGCGROWTHCONDITIONS
strain: GLBRCE1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded. PGCGROWTHCONDITIONS
SynH_LT_Trans_BXNC PGCGROWTHCONDITIONS
Total RNA (2ug) was subjected to rRNA depletion using Ribozero rRNA removal kit – Bacteria (Epicenter, illumina). rRNA-depleted RNA was purified using Ampure XP beads. Purified RNA was then fragmented using RNA Fragmentation Reagents (Ambion) at 70C for 2mins, targeting fragments ranging from 200-300bp. Fragmented RNA was then purified using Ampure XP beads (Agencourt). Reverse transcription was performed using SuperScript II Reverse Transcription (Invitrogen) with an initial annealing of random hexamers (Fermentas) at 65C for 5mins, follow by an incubation of 42C for 50mins and an inactivation step at 70C for 10mins. cDNA was then purified with Ampure XP beads. This was followed by second strand synthesis using dNTP mix where dTTP is replaced by dUTP. Reaction was performed at 16C for 1h. Double stranded cDNA fragments were purified and selected for targeted fragments (200-300bp) using Ampure XP beads. The dscDNA were then blunt-ended, the 3' ends were adenylated with a single A, and ligated with library adapters using Kapa Library Amplification Kit (Kapa Biosystems). Adapter-ligated DNA was purified using Ampure XP beads. Digestion of dUTP was then performed using AmpErase UNG (Applied Biosystems) to remove second strand cDNA. Digested cDNA was again cleaned up with Ampure SPRI beads. This was followed by amplification by 10 cycles of PCR using Kapa Library Amplification Kit (Kapa Biosystems). The final library was cleaned up with Ampure SPRI beads. Sequencing was done on the Illumina HiSeq platform generating paired end reads of 100bp each. Note: Target fragments here refers to the insert only, that is the cDNA.  The actual size we use in selection will be larger, typically the target fragment size + 125bp adaptors (~300-450bp). PGCGROWTHCONDITIONS
Basecalling was done on the sequencers using the sequencer's Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format. PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C. PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FASTQ formatted sequence files from strand-specific Illumina RNA-Seq reads were aligned to the GLBRCE1 reference genome NC_000913 using Bowtie version 0.12.7(Langmead et al., 2009) with '--nofw' strand-specific parameter and maximal distance between the paired reads of 1000 bp. NOTE: Genome NC_000913 (ASM584v2) represents the parental strain.  The strain used in our study was modified from the parental strain by replacing gene pflB with an insertion that contained 3 different genes. PGCGROWTHCONDITIONS
Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2 PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth phase: Trans PGCGROWTHCONDITIONS
medium: SynH_LT PGCGROWTHCONDITIONS
Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C PGCGROWTHCONDITIONS
strain: GLBRCE1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded. PGCGROWTHCONDITIONS
SynH_LT_Trans_BXXC PGCGROWTHCONDITIONS
Total RNA (2ug) was subjected to rRNA depletion using Ribozero rRNA removal kit – Bacteria (Epicenter, illumina). rRNA-depleted RNA was purified using Ampure XP beads. Purified RNA was then fragmented using RNA Fragmentation Reagents (Ambion) at 70C for 2mins, targeting fragments ranging from 200-300bp. Fragmented RNA was then purified using Ampure XP beads (Agencourt). Reverse transcription was performed using SuperScript II Reverse Transcription (Invitrogen) with an initial annealing of random hexamers (Fermentas) at 65C for 5mins, follow by an incubation of 42C for 50mins and an inactivation step at 70C for 10mins. cDNA was then purified with Ampure XP beads. This was followed by second strand synthesis using dNTP mix where dTTP is replaced by dUTP. Reaction was performed at 16C for 1h. Double stranded cDNA fragments were purified and selected for targeted fragments (200-300bp) using Ampure XP beads. The dscDNA were then blunt-ended, the 3' ends were adenylated with a single A, and ligated with library adapters using Kapa Library Amplification Kit (Kapa Biosystems). Adapter-ligated DNA was purified using Ampure XP beads. Digestion of dUTP was then performed using AmpErase UNG (Applied Biosystems) to remove second strand cDNA. Digested cDNA was again cleaned up with Ampure SPRI beads. This was followed by amplification by 10 cycles of PCR using Kapa Library Amplification Kit (Kapa Biosystems). The final library was cleaned up with Ampure SPRI beads. Sequencing was done on the Illumina HiSeq platform generating paired end reads of 100bp each. Note: Target fragments here refers to the insert only, that is the cDNA.  The actual size we use in selection will be larger, typically the target fragment size + 125bp adaptors (~300-450bp). PGCGROWTHCONDITIONS
Basecalling was done on the sequencers using the sequencer's Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format. PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C. PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FASTQ formatted sequence files from strand-specific Illumina RNA-Seq reads were aligned to the GLBRCE1 reference genome NC_000913 using Bowtie version 0.12.7(Langmead et al., 2009) with '--nofw' strand-specific parameter and maximal distance between the paired reads of 1000 bp. NOTE: Genome NC_000913 (ASM584v2) represents the parental strain.  The strain used in our study was modified from the parental strain by replacing gene pflB with an insertion that contained 3 different genes. PGCGROWTHCONDITIONS
Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2 PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth phase: Trans PGCGROWTHCONDITIONS
medium: SynH_LT PGCGROWTHCONDITIONS
Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C PGCGROWTHCONDITIONS
strain: GLBRCE1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded. PGCGROWTHCONDITIONS
SynH_LT_Trans_CBYW PGCGROWTHCONDITIONS
Total RNA (2ug) was subjected to rRNA depletion using Ribozero rRNA removal kit – Bacteria (Epicenter, illumina). rRNA-depleted RNA was purified using Ampure XP beads. Purified RNA was then fragmented using RNA Fragmentation Reagents (Ambion) at 70C for 2mins, targeting fragments ranging from 200-300bp. Fragmented RNA was then purified using Ampure XP beads (Agencourt). Reverse transcription was performed using SuperScript II Reverse Transcription (Invitrogen) with an initial annealing of random hexamers (Fermentas) at 65C for 5mins, follow by an incubation of 42C for 50mins and an inactivation step at 70C for 10mins. cDNA was then purified with Ampure XP beads. This was followed by second strand synthesis using dNTP mix where dTTP is replaced by dUTP. Reaction was performed at 16C for 1h. Double stranded cDNA fragments were purified and selected for targeted fragments (200-300bp) using Ampure XP beads. The dscDNA were then blunt-ended, the 3' ends were adenylated with a single A, and ligated with library adapters using Kapa Library Amplification Kit (Kapa Biosystems). Adapter-ligated DNA was purified using Ampure XP beads. Digestion of dUTP was then performed using AmpErase UNG (Applied Biosystems) to remove second strand cDNA. Digested cDNA was again cleaned up with Ampure SPRI beads. This was followed by amplification by 10 cycles of PCR using Kapa Library Amplification Kit (Kapa Biosystems). The final library was cleaned up with Ampure SPRI beads. Sequencing was done on the Illumina HiSeq platform generating paired end reads of 100bp each. Note: Target fragments here refers to the insert only, that is the cDNA.  The actual size we use in selection will be larger, typically the target fragment size + 125bp adaptors (~300-450bp). PGCGROWTHCONDITIONS
ACSH_Trans_CNFU PGCGROWTHCONDITIONS
Basecalling was done on the sequencers using the sequencer's Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format. PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C. PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FASTQ formatted sequence files from strand-specific Illumina RNA-Seq reads were aligned to the GLBRCE1 reference genome NC_000913 using Bowtie version 0.12.7(Langmead et al., 2009) with '--nofw' strand-specific parameter and maximal distance between the paired reads of 1000 bp. NOTE: Genome NC_000913 (ASM584v2) represents the parental strain.  The strain used in our study was modified from the parental strain by replacing gene pflB with an insertion that contained 3 different genes. PGCGROWTHCONDITIONS
Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2 PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth phase: Trans PGCGROWTHCONDITIONS
medium: ACSH PGCGROWTHCONDITIONS
Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C PGCGROWTHCONDITIONS
strain: GLBRCE1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded. PGCGROWTHCONDITIONS
Total RNA (2ug) was subjected to rRNA depletion using Ribozero rRNA removal kit – Bacteria (Epicenter, illumina). rRNA-depleted RNA was purified using Ampure XP beads. Purified RNA was then fragmented using RNA Fragmentation Reagents (Ambion) at 70C for 2mins, targeting fragments ranging from 200-300bp. Fragmented RNA was then purified using Ampure XP beads (Agencourt). Reverse transcription was performed using SuperScript II Reverse Transcription (Invitrogen) with an initial annealing of random hexamers (Fermentas) at 65C for 5mins, follow by an incubation of 42C for 50mins and an inactivation step at 70C for 10mins. cDNA was then purified with Ampure XP beads. This was followed by second strand synthesis using dNTP mix where dTTP is replaced by dUTP. Reaction was performed at 16C for 1h. Double stranded cDNA fragments were purified and selected for targeted fragments (200-300bp) using Ampure XP beads. The dscDNA were then blunt-ended, the 3' ends were adenylated with a single A, and ligated with library adapters using Kapa Library Amplification Kit (Kapa Biosystems). Adapter-ligated DNA was purified using Ampure XP beads. Digestion of dUTP was then performed using AmpErase UNG (Applied Biosystems) to remove second strand cDNA. Digested cDNA was again cleaned up with Ampure SPRI beads. This was followed by amplification by 10 cycles of PCR using Kapa Library Amplification Kit (Kapa Biosystems). The final library was cleaned up with Ampure SPRI beads. Sequencing was done on the Illumina HiSeq platform generating paired end reads of 100bp each. Note: Target fragments here refers to the insert only, that is the cDNA.  The actual size we use in selection will be larger, typically the target fragment size + 125bp adaptors (~300-450bp). PGCGROWTHCONDITIONS
ACSH_Trans_CIYT PGCGROWTHCONDITIONS
Basecalling was done on the sequencers using the sequencer's Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format. PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C. PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FASTQ formatted sequence files from strand-specific Illumina RNA-Seq reads were aligned to the GLBRCE1 reference genome NC_000913 using Bowtie version 0.12.7(Langmead et al., 2009) with '--nofw' strand-specific parameter and maximal distance between the paired reads of 1000 bp. NOTE: Genome NC_000913 (ASM584v2) represents the parental strain.  The strain used in our study was modified from the parental strain by replacing gene pflB with an insertion that contained 3 different genes. PGCGROWTHCONDITIONS
Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2 PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth phase: Trans PGCGROWTHCONDITIONS
medium: ACSH PGCGROWTHCONDITIONS
Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C PGCGROWTHCONDITIONS
strain: GLBRCE1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded. PGCGROWTHCONDITIONS
Total RNA (2ug) was subjected to rRNA depletion using Ribozero rRNA removal kit – Bacteria (Epicenter, illumina). rRNA-depleted RNA was purified using Ampure XP beads. Purified RNA was then fragmented using RNA Fragmentation Reagents (Ambion) at 70C for 2mins, targeting fragments ranging from 200-300bp. Fragmented RNA was then purified using Ampure XP beads (Agencourt). Reverse transcription was performed using SuperScript II Reverse Transcription (Invitrogen) with an initial annealing of random hexamers (Fermentas) at 65C for 5mins, follow by an incubation of 42C for 50mins and an inactivation step at 70C for 10mins. cDNA was then purified with Ampure XP beads. This was followed by second strand synthesis using dNTP mix where dTTP is replaced by dUTP. Reaction was performed at 16C for 1h. Double stranded cDNA fragments were purified and selected for targeted fragments (200-300bp) using Ampure XP beads. The dscDNA were then blunt-ended, the 3' ends were adenylated with a single A, and ligated with library adapters using Kapa Library Amplification Kit (Kapa Biosystems). Adapter-ligated DNA was purified using Ampure XP beads. Digestion of dUTP was then performed using AmpErase UNG (Applied Biosystems) to remove second strand cDNA. Digested cDNA was again cleaned up with Ampure SPRI beads. This was followed by amplification by 10 cycles of PCR using Kapa Library Amplification Kit (Kapa Biosystems). The final library was cleaned up with Ampure SPRI beads. Sequencing was done on the Illumina HiSeq platform generating paired end reads of 100bp each. Note: Target fragments here refers to the insert only, that is the cDNA.  The actual size we use in selection will be larger, typically the target fragment size + 125bp adaptors (~300-450bp). PGCGROWTHCONDITIONS
Basecalling was done on the sequencers using the sequencer's Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format. PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C. PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FASTQ formatted sequence files from strand-specific Illumina RNA-Seq reads were aligned to the GLBRCE1 reference genome NC_000913 using Bowtie version 0.12.7(Langmead et al., 2009) with '--nofw' strand-specific parameter and maximal distance between the paired reads of 1000 bp. NOTE: Genome NC_000913 (ASM584v2) represents the parental strain.  The strain used in our study was modified from the parental strain by replacing gene pflB with an insertion that contained 3 different genes. PGCGROWTHCONDITIONS
Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2 PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth phase: Stat1 PGCGROWTHCONDITIONS
medium: SynH PGCGROWTHCONDITIONS
Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C PGCGROWTHCONDITIONS
strain: GLBRCE1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded. PGCGROWTHCONDITIONS
SynH_Stat1_CBYN PGCGROWTHCONDITIONS
Total RNA (2ug) was subjected to rRNA depletion using Ribozero rRNA removal kit – Bacteria (Epicenter, illumina). rRNA-depleted RNA was purified using Ampure XP beads. Purified RNA was then fragmented using RNA Fragmentation Reagents (Ambion) at 70C for 2mins, targeting fragments ranging from 200-300bp. Fragmented RNA was then purified using Ampure XP beads (Agencourt). Reverse transcription was performed using SuperScript II Reverse Transcription (Invitrogen) with an initial annealing of random hexamers (Fermentas) at 65C for 5mins, follow by an incubation of 42C for 50mins and an inactivation step at 70C for 10mins. cDNA was then purified with Ampure XP beads. This was followed by second strand synthesis using dNTP mix where dTTP is replaced by dUTP. Reaction was performed at 16C for 1h. Double stranded cDNA fragments were purified and selected for targeted fragments (200-300bp) using Ampure XP beads. The dscDNA were then blunt-ended, the 3' ends were adenylated with a single A, and ligated with library adapters using Kapa Library Amplification Kit (Kapa Biosystems). Adapter-ligated DNA was purified using Ampure XP beads. Digestion of dUTP was then performed using AmpErase UNG (Applied Biosystems) to remove second strand cDNA. Digested cDNA was again cleaned up with Ampure SPRI beads. This was followed by amplification by 10 cycles of PCR using Kapa Library Amplification Kit (Kapa Biosystems). The final library was cleaned up with Ampure SPRI beads. Sequencing was done on the Illumina HiSeq platform generating paired end reads of 100bp each. Note: Target fragments here refers to the insert only, that is the cDNA.  The actual size we use in selection will be larger, typically the target fragment size + 125bp adaptors (~300-450bp). PGCGROWTHCONDITIONS
Basecalling was done on the sequencers using the sequencer's Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format. PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C. PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FASTQ formatted sequence files from strand-specific Illumina RNA-Seq reads were aligned to the GLBRCE1 reference genome NC_000913 using Bowtie version 0.12.7(Langmead et al., 2009) with '--nofw' strand-specific parameter and maximal distance between the paired reads of 1000 bp. NOTE: Genome NC_000913 (ASM584v2) represents the parental strain.  The strain used in our study was modified from the parental strain by replacing gene pflB with an insertion that contained 3 different genes. PGCGROWTHCONDITIONS
Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2 PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth phase: Stat1 PGCGROWTHCONDITIONS
medium: SynH PGCGROWTHCONDITIONS
Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C PGCGROWTHCONDITIONS
strain: GLBRCE1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded. PGCGROWTHCONDITIONS
SynH_Stat1_CUOC PGCGROWTHCONDITIONS
Total RNA (2ug) was subjected to rRNA depletion using Ribozero rRNA removal kit – Bacteria (Epicenter, illumina). rRNA-depleted RNA was purified using Ampure XP beads. Purified RNA was then fragmented using RNA Fragmentation Reagents (Ambion) at 70C for 2mins, targeting fragments ranging from 200-300bp. Fragmented RNA was then purified using Ampure XP beads (Agencourt). Reverse transcription was performed using SuperScript II Reverse Transcription (Invitrogen) with an initial annealing of random hexamers (Fermentas) at 65C for 5mins, follow by an incubation of 42C for 50mins and an inactivation step at 70C for 10mins. cDNA was then purified with Ampure XP beads. This was followed by second strand synthesis using dNTP mix where dTTP is replaced by dUTP. Reaction was performed at 16C for 1h. Double stranded cDNA fragments were purified and selected for targeted fragments (200-300bp) using Ampure XP beads. The dscDNA were then blunt-ended, the 3' ends were adenylated with a single A, and ligated with library adapters using Kapa Library Amplification Kit (Kapa Biosystems). Adapter-ligated DNA was purified using Ampure XP beads. Digestion of dUTP was then performed using AmpErase UNG (Applied Biosystems) to remove second strand cDNA. Digested cDNA was again cleaned up with Ampure SPRI beads. This was followed by amplification by 10 cycles of PCR using Kapa Library Amplification Kit (Kapa Biosystems). The final library was cleaned up with Ampure SPRI beads. Sequencing was done on the Illumina HiSeq platform generating paired end reads of 100bp each. Note: Target fragments here refers to the insert only, that is the cDNA.  The actual size we use in selection will be larger, typically the target fragment size + 125bp adaptors (~300-450bp). PGCGROWTHCONDITIONS
Basecalling was done on the sequencers using the sequencer's Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format. PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C. PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FASTQ formatted sequence files from strand-specific Illumina RNA-Seq reads were aligned to the GLBRCE1 reference genome NC_000913 using Bowtie version 0.12.7(Langmead et al., 2009) with '--nofw' strand-specific parameter and maximal distance between the paired reads of 1000 bp. NOTE: Genome NC_000913 (ASM584v2) represents the parental strain.  The strain used in our study was modified from the parental strain by replacing gene pflB with an insertion that contained 3 different genes. PGCGROWTHCONDITIONS
Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2 PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth phase: Stat1 PGCGROWTHCONDITIONS
medium: SynH_LT PGCGROWTHCONDITIONS
Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C PGCGROWTHCONDITIONS
strain: GLBRCE1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded. PGCGROWTHCONDITIONS
SynH_LT_Stat1_BXNB PGCGROWTHCONDITIONS
Total RNA (2ug) was subjected to rRNA depletion using Ribozero rRNA removal kit – Bacteria (Epicenter, illumina). rRNA-depleted RNA was purified using Ampure XP beads. Purified RNA was then fragmented using RNA Fragmentation Reagents (Ambion) at 70C for 2mins, targeting fragments ranging from 200-300bp. Fragmented RNA was then purified using Ampure XP beads (Agencourt). Reverse transcription was performed using SuperScript II Reverse Transcription (Invitrogen) with an initial annealing of random hexamers (Fermentas) at 65C for 5mins, follow by an incubation of 42C for 50mins and an inactivation step at 70C for 10mins. cDNA was then purified with Ampure XP beads. This was followed by second strand synthesis using dNTP mix where dTTP is replaced by dUTP. Reaction was performed at 16C for 1h. Double stranded cDNA fragments were purified and selected for targeted fragments (200-300bp) using Ampure XP beads. The dscDNA were then blunt-ended, the 3' ends were adenylated with a single A, and ligated with library adapters using Kapa Library Amplification Kit (Kapa Biosystems). Adapter-ligated DNA was purified using Ampure XP beads. Digestion of dUTP was then performed using AmpErase UNG (Applied Biosystems) to remove second strand cDNA. Digested cDNA was again cleaned up with Ampure SPRI beads. This was followed by amplification by 10 cycles of PCR using Kapa Library Amplification Kit (Kapa Biosystems). The final library was cleaned up with Ampure SPRI beads. Sequencing was done on the Illumina HiSeq platform generating paired end reads of 100bp each. Note: Target fragments here refers to the insert only, that is the cDNA.  The actual size we use in selection will be larger, typically the target fragment size + 125bp adaptors (~300-450bp). PGCGROWTHCONDITIONS
Basecalling was done on the sequencers using the sequencer's Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format. PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C. PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FASTQ formatted sequence files from strand-specific Illumina RNA-Seq reads were aligned to the GLBRCE1 reference genome NC_000913 using Bowtie version 0.12.7(Langmead et al., 2009) with '--nofw' strand-specific parameter and maximal distance between the paired reads of 1000 bp. NOTE: Genome NC_000913 (ASM584v2) represents the parental strain.  The strain used in our study was modified from the parental strain by replacing gene pflB with an insertion that contained 3 different genes. PGCGROWTHCONDITIONS
Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2 PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth phase: Stat1 PGCGROWTHCONDITIONS
medium: SynH_LT PGCGROWTHCONDITIONS
Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C PGCGROWTHCONDITIONS
strain: GLBRCE1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded. PGCGROWTHCONDITIONS
SynH_LT_Stat1_BXNZ PGCGROWTHCONDITIONS
Total RNA (2ug) was subjected to rRNA depletion using Ribozero rRNA removal kit – Bacteria (Epicenter, illumina). rRNA-depleted RNA was purified using Ampure XP beads. Purified RNA was then fragmented using RNA Fragmentation Reagents (Ambion) at 70C for 2mins, targeting fragments ranging from 200-300bp. Fragmented RNA was then purified using Ampure XP beads (Agencourt). Reverse transcription was performed using SuperScript II Reverse Transcription (Invitrogen) with an initial annealing of random hexamers (Fermentas) at 65C for 5mins, follow by an incubation of 42C for 50mins and an inactivation step at 70C for 10mins. cDNA was then purified with Ampure XP beads. This was followed by second strand synthesis using dNTP mix where dTTP is replaced by dUTP. Reaction was performed at 16C for 1h. Double stranded cDNA fragments were purified and selected for targeted fragments (200-300bp) using Ampure XP beads. The dscDNA were then blunt-ended, the 3' ends were adenylated with a single A, and ligated with library adapters using Kapa Library Amplification Kit (Kapa Biosystems). Adapter-ligated DNA was purified using Ampure XP beads. Digestion of dUTP was then performed using AmpErase UNG (Applied Biosystems) to remove second strand cDNA. Digested cDNA was again cleaned up with Ampure SPRI beads. This was followed by amplification by 10 cycles of PCR using Kapa Library Amplification Kit (Kapa Biosystems). The final library was cleaned up with Ampure SPRI beads. Sequencing was done on the Illumina HiSeq platform generating paired end reads of 100bp each. Note: Target fragments here refers to the insert only, that is the cDNA.  The actual size we use in selection will be larger, typically the target fragment size + 125bp adaptors (~300-450bp). PGCGROWTHCONDITIONS
Basecalling was done on the sequencers using the sequencer's Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format. PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C. PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FASTQ formatted sequence files from strand-specific Illumina RNA-Seq reads were aligned to the GLBRCE1 reference genome NC_000913 using Bowtie version 0.12.7(Langmead et al., 2009) with '--nofw' strand-specific parameter and maximal distance between the paired reads of 1000 bp. NOTE: Genome NC_000913 (ASM584v2) represents the parental strain.  The strain used in our study was modified from the parental strain by replacing gene pflB with an insertion that contained 3 different genes. PGCGROWTHCONDITIONS
Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2 PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth phase: Stat1 PGCGROWTHCONDITIONS
medium: SynH_LT PGCGROWTHCONDITIONS
Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C PGCGROWTHCONDITIONS
strain: GLBRCE1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded. PGCGROWTHCONDITIONS
SynH_LT_Stat1_CHBW PGCGROWTHCONDITIONS
Total RNA (2ug) was subjected to rRNA depletion using Ribozero rRNA removal kit – Bacteria (Epicenter, illumina). rRNA-depleted RNA was purified using Ampure XP beads. Purified RNA was then fragmented using RNA Fragmentation Reagents (Ambion) at 70C for 2mins, targeting fragments ranging from 200-300bp. Fragmented RNA was then purified using Ampure XP beads (Agencourt). Reverse transcription was performed using SuperScript II Reverse Transcription (Invitrogen) with an initial annealing of random hexamers (Fermentas) at 65C for 5mins, follow by an incubation of 42C for 50mins and an inactivation step at 70C for 10mins. cDNA was then purified with Ampure XP beads. This was followed by second strand synthesis using dNTP mix where dTTP is replaced by dUTP. Reaction was performed at 16C for 1h. Double stranded cDNA fragments were purified and selected for targeted fragments (200-300bp) using Ampure XP beads. The dscDNA were then blunt-ended, the 3' ends were adenylated with a single A, and ligated with library adapters using Kapa Library Amplification Kit (Kapa Biosystems). Adapter-ligated DNA was purified using Ampure XP beads. Digestion of dUTP was then performed using AmpErase UNG (Applied Biosystems) to remove second strand cDNA. Digested cDNA was again cleaned up with Ampure SPRI beads. This was followed by amplification by 10 cycles of PCR using Kapa Library Amplification Kit (Kapa Biosystems). The final library was cleaned up with Ampure SPRI beads. Sequencing was done on the Illumina HiSeq platform generating paired end reads of 100bp each. Note: Target fragments here refers to the insert only, that is the cDNA.  The actual size we use in selection will be larger, typically the target fragment size + 125bp adaptors (~300-450bp). PGCGROWTHCONDITIONS
ACSH_Stat1_CNFW PGCGROWTHCONDITIONS
Basecalling was done on the sequencers using the sequencer's Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format. PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C. PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FASTQ formatted sequence files from strand-specific Illumina RNA-Seq reads were aligned to the GLBRCE1 reference genome NC_000913 using Bowtie version 0.12.7(Langmead et al., 2009) with '--nofw' strand-specific parameter and maximal distance between the paired reads of 1000 bp. NOTE: Genome NC_000913 (ASM584v2) represents the parental strain.  The strain used in our study was modified from the parental strain by replacing gene pflB with an insertion that contained 3 different genes. PGCGROWTHCONDITIONS
Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2 PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth phase: Stat1 PGCGROWTHCONDITIONS
medium: ACSH PGCGROWTHCONDITIONS
Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C PGCGROWTHCONDITIONS
strain: GLBRCE1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded. PGCGROWTHCONDITIONS
Total RNA (2ug) was subjected to rRNA depletion using Ribozero rRNA removal kit – Bacteria (Epicenter, illumina). rRNA-depleted RNA was purified using Ampure XP beads. Purified RNA was then fragmented using RNA Fragmentation Reagents (Ambion) at 70C for 2mins, targeting fragments ranging from 200-300bp. Fragmented RNA was then purified using Ampure XP beads (Agencourt). Reverse transcription was performed using SuperScript II Reverse Transcription (Invitrogen) with an initial annealing of random hexamers (Fermentas) at 65C for 5mins, follow by an incubation of 42C for 50mins and an inactivation step at 70C for 10mins. cDNA was then purified with Ampure XP beads. This was followed by second strand synthesis using dNTP mix where dTTP is replaced by dUTP. Reaction was performed at 16C for 1h. Double stranded cDNA fragments were purified and selected for targeted fragments (200-300bp) using Ampure XP beads. The dscDNA were then blunt-ended, the 3' ends were adenylated with a single A, and ligated with library adapters using Kapa Library Amplification Kit (Kapa Biosystems). Adapter-ligated DNA was purified using Ampure XP beads. Digestion of dUTP was then performed using AmpErase UNG (Applied Biosystems) to remove second strand cDNA. Digested cDNA was again cleaned up with Ampure SPRI beads. This was followed by amplification by 10 cycles of PCR using Kapa Library Amplification Kit (Kapa Biosystems). The final library was cleaned up with Ampure SPRI beads. Sequencing was done on the Illumina HiSeq platform generating paired end reads of 100bp each. Note: Target fragments here refers to the insert only, that is the cDNA.  The actual size we use in selection will be larger, typically the target fragment size + 125bp adaptors (~300-450bp). PGCGROWTHCONDITIONS
ACSH_Stat1_CNGG PGCGROWTHCONDITIONS
Basecalling was done on the sequencers using the sequencer's Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format. PGCGROWTHCONDITIONS
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C. PGCGROWTHCONDITIONS
Escherichia coli GLBRCE1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FASTQ formatted sequence files from strand-specific Illumina RNA-Seq reads were aligned to the GLBRCE1 reference genome NC_000913 using Bowtie version 0.12.7(Langmead et al., 2009) with '--nofw' strand-specific parameter and maximal distance between the paired reads of 1000 bp. NOTE: Genome NC_000913 (ASM584v2) represents the parental strain.  The strain used in our study was modified from the parental strain by replacing gene pflB with an insertion that contained 3 different genes. PGCGROWTHCONDITIONS
Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2 PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth phase: Stat1 PGCGROWTHCONDITIONS
medium: ACSH PGCGROWTHCONDITIONS
Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C PGCGROWTHCONDITIONS
strain: GLBRCE1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded. PGCGROWTHCONDITIONS
Total RNA (2ug) was subjected to rRNA depletion using Ribozero rRNA removal kit – Bacteria (Epicenter, illumina). rRNA-depleted RNA was purified using Ampure XP beads. Purified RNA was then fragmented using RNA Fragmentation Reagents (Ambion) at 70C for 2mins, targeting fragments ranging from 200-300bp. Fragmented RNA was then purified using Ampure XP beads (Agencourt). Reverse transcription was performed using SuperScript II Reverse Transcription (Invitrogen) with an initial annealing of random hexamers (Fermentas) at 65C for 5mins, follow by an incubation of 42C for 50mins and an inactivation step at 70C for 10mins. cDNA was then purified with Ampure XP beads. This was followed by second strand synthesis using dNTP mix where dTTP is replaced by dUTP. Reaction was performed at 16C for 1h. Double stranded cDNA fragments were purified and selected for targeted fragments (200-300bp) using Ampure XP beads. The dscDNA were then blunt-ended, the 3' ends were adenylated with a single A, and ligated with library adapters using Kapa Library Amplification Kit (Kapa Biosystems). Adapter-ligated DNA was purified using Ampure XP beads. Digestion of dUTP was then performed using AmpErase UNG (Applied Biosystems) to remove second strand cDNA. Digested cDNA was again cleaned up with Ampure SPRI beads. This was followed by amplification by 10 cycles of PCR using Kapa Library Amplification Kit (Kapa Biosystems). The final library was cleaned up with Ampure SPRI beads. Sequencing was done on the Illumina HiSeq platform generating paired end reads of 100bp each. Note: Target fragments here refers to the insert only, that is the cDNA.  The actual size we use in selection will be larger, typically the target fragment size + 125bp adaptors (~300-450bp). PGCGROWTHCONDITIONS
1 ml of each culture with the mycotoxin was centrifuged and total RNA was prepared using Hybrid-RTM kit (Gene All, Seoul, Korea) according to the manufacturer’s protocols. A MICOBExpressTM bacterial mRNA enrichment kit (Ambion, Texas, USA) was used to remove bacterial rRNA from the total RNA samples. PGCGROWTHCONDITIONS
acetonitrile PGCGROWTHCONDITIONS
Bacterial culture with acetonitrile PGCGROWTHCONDITIONS
condition: acetonitrile (control) PGCGROWTHCONDITIONS
E. coli K-12 was incubated in 5 ml LB liquid for 16 h at 37°C with constant shaking, and then 100 µl of each myxotoxin dissolved in acetonitrile was added to each culture to a final concentration of 0.2, and 2 ppm. Additional incubation was performed for 2 h. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K-12 substr. DH10B ASM1942v1 PGCGROWTHCONDITIONS
Mapped reads per annotated gene were counted by Bam2readcount. PGCGROWTHCONDITIONS
Reads per kilobase of gene per million mapped sequence reads (RPKM) were calculated for normalization. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 substr. DH10B PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: txt: tab-delimited text files include RPKM values for each Sample PGCGROWTHCONDITIONS
The reads were processed using BWA software. PGCGROWTHCONDITIONS
0.2 ppm deoxynivalenol PGCGROWTHCONDITIONS
1 ml of each culture with the mycotoxin was centrifuged and total RNA was prepared using Hybrid-RTM kit (Gene All, Seoul, Korea) according to the manufacturer’s protocols. A MICOBExpressTM bacterial mRNA enrichment kit (Ambion, Texas, USA) was used to remove bacterial rRNA from the total RNA samples. PGCGROWTHCONDITIONS
Bacterial culture with 0.2 ppm deoxynivalenol PGCGROWTHCONDITIONS
concentration: 0.2 ppm PGCGROWTHCONDITIONS
condition: myxotoxin PGCGROWTHCONDITIONS
E. coli K-12 was incubated in 5 ml LB liquid for 16 h at 37°C with constant shaking, and then 100 µl of each myxotoxin dissolved in acetonitrile was added to each culture to a final concentration of 0.2, and 2 ppm. Additional incubation was performed for 2 h. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K-12 substr. DH10B ASM1942v1 PGCGROWTHCONDITIONS
Mapped reads per annotated gene were counted by Bam2readcount. PGCGROWTHCONDITIONS
Reads per kilobase of gene per million mapped sequence reads (RPKM) were calculated for normalization. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 substr. DH10B PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: txt: tab-delimited text files include RPKM values for each Sample PGCGROWTHCONDITIONS
The reads were processed using BWA software. PGCGROWTHCONDITIONS
toxin: deoxynivalenol PGCGROWTHCONDITIONS
1 ml of each culture with the mycotoxin was centrifuged and total RNA was prepared using Hybrid-RTM kit (Gene All, Seoul, Korea) according to the manufacturer’s protocols. A MICOBExpressTM bacterial mRNA enrichment kit (Ambion, Texas, USA) was used to remove bacterial rRNA from the total RNA samples. PGCGROWTHCONDITIONS
2 ppm deoxynivalenol PGCGROWTHCONDITIONS
Bacterial culture with 2 ppm deoxynivalenol PGCGROWTHCONDITIONS
concentration: 2 ppm PGCGROWTHCONDITIONS
condition: myxotoxin PGCGROWTHCONDITIONS
E. coli K-12 was incubated in 5 ml LB liquid for 16 h at 37°C with constant shaking, and then 100 µl of each myxotoxin dissolved in acetonitrile was added to each culture to a final concentration of 0.2, and 2 ppm. Additional incubation was performed for 2 h. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K-12 substr. DH10B ASM1942v1 PGCGROWTHCONDITIONS
Mapped reads per annotated gene were counted by Bam2readcount. PGCGROWTHCONDITIONS
Reads per kilobase of gene per million mapped sequence reads (RPKM) were calculated for normalization. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 substr. DH10B PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: txt: tab-delimited text files include RPKM values for each Sample PGCGROWTHCONDITIONS
The reads were processed using BWA software. PGCGROWTHCONDITIONS
toxin: deoxynivalenol PGCGROWTHCONDITIONS
0.2 ppm nivalenol PGCGROWTHCONDITIONS
1 ml of each culture with the mycotoxin was centrifuged and total RNA was prepared using Hybrid-RTM kit (Gene All, Seoul, Korea) according to the manufacturer’s protocols. A MICOBExpressTM bacterial mRNA enrichment kit (Ambion, Texas, USA) was used to remove bacterial rRNA from the total RNA samples. PGCGROWTHCONDITIONS
Bacterial culture with 0.2 ppm nivalenol PGCGROWTHCONDITIONS
concentration: 0.2 ppm PGCGROWTHCONDITIONS
condition: myxotoxin PGCGROWTHCONDITIONS
E. coli K-12 was incubated in 5 ml LB liquid for 16 h at 37°C with constant shaking, and then 100 µl of each myxotoxin dissolved in acetonitrile was added to each culture to a final concentration of 0.2, and 2 ppm. Additional incubation was performed for 2 h. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K-12 substr. DH10B ASM1942v1 PGCGROWTHCONDITIONS
Mapped reads per annotated gene were counted by Bam2readcount. PGCGROWTHCONDITIONS
Reads per kilobase of gene per million mapped sequence reads (RPKM) were calculated for normalization. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 substr. DH10B PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: txt: tab-delimited text files include RPKM values for each Sample PGCGROWTHCONDITIONS
The reads were processed using BWA software. PGCGROWTHCONDITIONS
toxin: nivalenol PGCGROWTHCONDITIONS
1 ml of each culture with the mycotoxin was centrifuged and total RNA was prepared using Hybrid-RTM kit (Gene All, Seoul, Korea) according to the manufacturer’s protocols. A MICOBExpressTM bacterial mRNA enrichment kit (Ambion, Texas, USA) was used to remove bacterial rRNA from the total RNA samples. PGCGROWTHCONDITIONS
2 ppm nivalenol PGCGROWTHCONDITIONS
Bacterial culture with 2 ppm nivalenol PGCGROWTHCONDITIONS
concentration: 2 ppm PGCGROWTHCONDITIONS
condition: myxotoxin PGCGROWTHCONDITIONS
E. coli K-12 was incubated in 5 ml LB liquid for 16 h at 37°C with constant shaking, and then 100 µl of each myxotoxin dissolved in acetonitrile was added to each culture to a final concentration of 0.2, and 2 ppm. Additional incubation was performed for 2 h. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli K-12 substr. DH10B ASM1942v1 PGCGROWTHCONDITIONS
Mapped reads per annotated gene were counted by Bam2readcount. PGCGROWTHCONDITIONS
Reads per kilobase of gene per million mapped sequence reads (RPKM) were calculated for normalization. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 substr. DH10B PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: txt: tab-delimited text files include RPKM values for each Sample PGCGROWTHCONDITIONS
The reads were processed using BWA software. PGCGROWTHCONDITIONS
toxin: nivalenol PGCGROWTHCONDITIONS
Culture cells PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
genotype: Wild-type PGCGROWTHCONDITIONS
growth phase: Exponential Phase PGCGROWTHCONDITIONS
Overnight cultures from isolated colonies were diluted in fresh medium to an initial OD600~0.03 and grown to exponential phase (OD600~0.3) at 37ºC, with shaking at 200 rpm in Luria-Bertani (LB) medium supplemented with thymine (50 mg ml-1). When required, antibiotics were present at the following concentrations: kanamycin, 50 mg ml-1; tetracycline, 20 mg ml-1; streptomycin/spectinomycin 20 µg ml-1. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing by the company Vertis Biotechnologie AG in Germany PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated following cell lysis and phenol:chloroform extraction as previously described (Andrade, Pobre et al. 2012). After precipitation step in ethanol and 300 mM sodium acetate, RNA was resuspended in MilliQ-water. The integrity of RNA samples was evaluated by agarose gel electrophoresis. Turbo DNase (Ambion) treatment was used to remove contaminant DNA. PGCGROWTHCONDITIONS
strain: K12-MG1693 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample … PGCGROWTHCONDITIONS
Vertis Biotechnologie AG bioinformatics department did a preliminary analysis of the high-throughput sequencing results which included the mapping of the reads against E. coli genome (NC_000913 downloaded from NCBI genome database). PGCGROWTHCONDITIONS
We then used the mapped files to run Cufflinks (estimates the relative abundance of the transcripts) and after Cuffdiff to find significant changes in transcript expression when comparing two samples (Trapnell, Williams et al. 2010). PGCGROWTHCONDITIONS
WT_RNA-Seq PGCGROWTHCONDITIONS
Culture cells PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
genotype: RNase II mutant PGCGROWTHCONDITIONS
growth phase: Exponential Phase PGCGROWTHCONDITIONS
Overnight cultures from isolated colonies were diluted in fresh medium to an initial OD600~0.03 and grown to exponential phase (OD600~0.3) at 37ºC, with shaking at 200 rpm in Luria-Bertani (LB) medium supplemented with thymine (50 mg ml-1). When required, antibiotics were present at the following concentrations: kanamycin, 50 mg ml-1; tetracycline, 20 mg ml-1; streptomycin/spectinomycin 20 µg ml-1. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing by the company Vertis Biotechnologie AG in Germany PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated following cell lysis and phenol:chloroform extraction as previously described (Andrade, Pobre et al. 2012). After precipitation step in ethanol and 300 mM sodium acetate, RNA was resuspended in MilliQ-water. The integrity of RNA samples was evaluated by agarose gel electrophoresis. Turbo DNase (Ambion) treatment was used to remove contaminant DNA. PGCGROWTHCONDITIONS
∆rnb_RNA-Seq PGCGROWTHCONDITIONS
strain: K12-MG1693 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample … PGCGROWTHCONDITIONS
Vertis Biotechnologie AG bioinformatics department did a preliminary analysis of the high-throughput sequencing results which included the mapping of the reads against E. coli genome (NC_000913 downloaded from NCBI genome database). PGCGROWTHCONDITIONS
We then used the mapped files to run Cufflinks (estimates the relative abundance of the transcripts) and after Cuffdiff to find significant changes in transcript expression when comparing two samples (Trapnell, Williams et al. 2010). PGCGROWTHCONDITIONS
Culture cells PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
genotype: RNase R mutant PGCGROWTHCONDITIONS
growth phase: Exponential Phase PGCGROWTHCONDITIONS
Overnight cultures from isolated colonies were diluted in fresh medium to an initial OD600~0.03 and grown to exponential phase (OD600~0.3) at 37ºC, with shaking at 200 rpm in Luria-Bertani (LB) medium supplemented with thymine (50 mg ml-1). When required, antibiotics were present at the following concentrations: kanamycin, 50 mg ml-1; tetracycline, 20 mg ml-1; streptomycin/spectinomycin 20 µg ml-1. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing by the company Vertis Biotechnologie AG in Germany PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated following cell lysis and phenol:chloroform extraction as previously described (Andrade, Pobre et al. 2012). After precipitation step in ethanol and 300 mM sodium acetate, RNA was resuspended in MilliQ-water. The integrity of RNA samples was evaluated by agarose gel electrophoresis. Turbo DNase (Ambion) treatment was used to remove contaminant DNA. PGCGROWTHCONDITIONS
∆rnr_RNA-Seq PGCGROWTHCONDITIONS
strain: K12-MG1693 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample … PGCGROWTHCONDITIONS
Vertis Biotechnologie AG bioinformatics department did a preliminary analysis of the high-throughput sequencing results which included the mapping of the reads against E. coli genome (NC_000913 downloaded from NCBI genome database). PGCGROWTHCONDITIONS
We then used the mapped files to run Cufflinks (estimates the relative abundance of the transcripts) and after Cuffdiff to find significant changes in transcript expression when comparing two samples (Trapnell, Williams et al. 2010). PGCGROWTHCONDITIONS
Culture cells PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
genotype: PNPase mutant PGCGROWTHCONDITIONS
growth phase: Exponential Phase PGCGROWTHCONDITIONS
Overnight cultures from isolated colonies were diluted in fresh medium to an initial OD600~0.03 and grown to exponential phase (OD600~0.3) at 37ºC, with shaking at 200 rpm in Luria-Bertani (LB) medium supplemented with thymine (50 mg ml-1). When required, antibiotics were present at the following concentrations: kanamycin, 50 mg ml-1; tetracycline, 20 mg ml-1; streptomycin/spectinomycin 20 µg ml-1. PGCGROWTHCONDITIONS
∆pnp_RNA-Seq PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing by the company Vertis Biotechnologie AG in Germany PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated following cell lysis and phenol:chloroform extraction as previously described (Andrade, Pobre et al. 2012). After precipitation step in ethanol and 300 mM sodium acetate, RNA was resuspended in MilliQ-water. The integrity of RNA samples was evaluated by agarose gel electrophoresis. Turbo DNase (Ambion) treatment was used to remove contaminant DNA. PGCGROWTHCONDITIONS
strain: K12-MG1693 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample … PGCGROWTHCONDITIONS
Vertis Biotechnologie AG bioinformatics department did a preliminary analysis of the high-throughput sequencing results which included the mapping of the reads against E. coli genome (NC_000913 downloaded from NCBI genome database). PGCGROWTHCONDITIONS
We then used the mapped files to run Cufflinks (estimates the relative abundance of the transcripts) and after Cuffdiff to find significant changes in transcript expression when comparing two samples (Trapnell, Williams et al. 2010). PGCGROWTHCONDITIONS
cDNA library of the nascent RNA was constructed according to Churchman and Weissman, Nature 2011 (PMID: 21248844). PGCGROWTHCONDITIONS
Each tube of the cell pellet stored at -80˚C was resuspended in 650 ml TES buffer (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 100 mM NaCl, 0.1% TritonX 100, 0.3 mM PMSF) at room temperature (RT). The cell suspension was mixed with 100 kU Ready-Lyse Lysozyme (Epicentre) and 50 µg RNaseA (Sigma) and incubated for 5 min, allowing rapid cell lysis. To digest the nucleoide, 62.5 U DNaseI (Roche) and 250 µg/ml heparin at the final concentrations as well as 74 ml DNaseI buffer (10 mM MnCl2 10 mM Tris-HCl, pH 7.5) were added to the mixture and incubated for 10 min at RT. To remove cell debris, the mixture was centrifuged at 20,000 x g for 3 min at 4˚C and the supernatant was collected into a new 1.5 ml tube. The supernatant including RNAPs that form ternary complexes with RNA/DNA were immobilized on ~155 µl Ni-NTA agarose (Qiagen) pre-equilibrated with the binding buffer (0.5 M NaCl, 5 mM imidazole, 5% glycerol, 20 mM Tris-HCl, pH7.9, 1 mM 2-mercaptoethanol) with shaking for 10 min at 4˚C. The immobilized ternary complexes were washed five times with the wash buffer (1M NaCl, 15 mM imidazole, 5% glycerol, pH7.9, 1 mM 2-mercaptoethanol) at 4˚C, washed twice with the nuclease buffer (40 mM KCl, 15 mM imidazole, 20 mM Tris-HCl, pH 7.9, 0.3 mM MgCl2 5% glycerol, 1 mM 2-mercaptoethanol) at 4˚C. The RNA transcript and DNA unprotected by RNAP were cleaved by the additions of 0.4 U RNase V1 (Invitrogen), 0.7 U RNase T1 (Sigma), and 5 U DNase I (Takara Bio) to the immobilized complexes and incubation for 7 min at RT. The nuclease-treated complexes were washed twice with the wash buffer, twice with the MnCl2-free nuclease buffer at 4˚C, and eluted by increasing the concentration of imidazole to 100 mM followed by shaking for 10 min at 4˚C in the presence of 30 U SUPERase RNase inhibitor (Ambion). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype/variation: W3110 rpoC-6xHis::kan greA::tet, greB::amp PGCGROWTHCONDITIONS
molecule subtype: nascent 3' RNA PGCGROWTHCONDITIONS
Pause sites in E. coli ΔgreAB strain identified by RNET-seq PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
The 200 ml eluate from the Ni-NTA agarose was mixed with equal volume of pre-warmed PCI and incubated for 2 min at 70˚C. The mixture was centrifuged, and RNA and DNA were precipitated with isopropanol from the supernatant. The pellet was dissolved in 30 ml DNase I buffer with 5 U DNaseI (Takara Bio) and 20 U SUPERase, incubated for 10 min at RT. RNA was separated from the digested DNA by the PCI extraction and RNA was precipitated with isopropanol. The pellet was dissolved in diethylpyrocarbonate-treated water and used for cDNA synthesis. PGCGROWTHCONDITIONS
The cells were grown in ~300 ml LB broth +25 mg/ml kanamycin with shaking at 37˚C until OD600 of ~0.5.The cells of 150 mg (wet weight) were harvested by centrifugation at 6,500 × g for 4 min at 4˚C, aliquoted in three 1.5 ml tubes, flash frozen in liquid nitrogen, and stored at -80˚C. PGCGROWTHCONDITIONS
The fastq files of 36-bp sequenced reads were generated with the CASAVA v1.8 (Illumina). For the bulk RNET-seq analysis, the specific adapter sequences were trimmed with the Trimmomatic v0.25 to obtain reads ≥ 21-nt from the 5’ end. The reads ≥ 21-nt were mapped to the reference genome of E. coli K-12 strain W3110 (NC_007779.1) using the Bowtie2 v2.1.0 with the default parameter. A gene annotation file of E. coli W3110 was downloaded from the ftp server of Ensembl. PGCGROWTHCONDITIONS
The processed data file (csv) includes information about genomic position, reference/non-reference bases, read count, the fraction of 3’ RNA end, DNA strand (+/-), gene name, and mapping/base qualities in transcriptional pause sites that are defined by the parameters P(0.9, 160). PGCGROWTHCONDITIONS
To analyze RNAP pausing on the E. coli chromosome, we counted the number of reads at every genomic nucleotide position using the mpileup command of SAM tools v0.1.18 with –A –B parameters. Pausing sites were defined P(φ, δ), where φ is the minimal fraction of having 3’ RNA ends in the mapped reads and δ is the minimal read depth for any genomic position. We chose δ to be 100 for WT and 160 for ΔgreAB, which normalized these respective numbers for each strain since there were 1.6-fold more total reads in the ΔgreAB strain. The high φ parameter allowed us to define a reliable pause-inducing element for WT or ΔgreAB cells. PGCGROWTHCONDITIONS
W3110 rpoC-6xHis::kan greA::tet, greB::amp PGCGROWTHCONDITIONS
10 μg of total RNA sample was subjected to purification for discarding rRNA via the MICROBExpress kit (Ambion) according to the manufacturer’s protocol. Following purification, the RNA was interrupted into short fragments using divalent cations under elevated temperature and the short fragments were used for the cDNA synthesis using a SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) according to the manufacturer’s instructions. These cDNA fragments were purified with a QIAquick PCR purification kit (Qiagen), and then went through end reparation, adding poly(A) and ligation of sequencing adaptors. These products were purified with agarose gel electrophoresis and fragments in the size of 200-250 bp were selected for PCR amplification to construct the cDNA library. PGCGROWTHCONDITIONS
All those uniquely mapped reads were used to calculate the gene expression level by the RPKM method, which is able to eliminate the influence of different gene length and sequencing discrepancy on the calculation of gene expression and thus the calculated gene expression level can be directly used for comparing the difference of gene expression among samples. PGCGROWTHCONDITIONS
Bacterium PGCGROWTHCONDITIONS
Base calling performed using  Illumina GA pipeline 1.6. PGCGROWTHCONDITIONS
con_RNAA PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: ASM666v1; NC_002655.2 PGCGROWTHCONDITIONS
In order to generate the VBNC state in E. coli O157:H7, 20 mL of the exponential-phase cell suspensions in a 50 mL sterile glass tube was treated by HPCD at 5 MPa and 25℃ for 40 min. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: O157:H7 NCTC 12900 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Microsoft excel spreadsheet files include RPKM values for each gene of sample PGCGROWTHCONDITIONS
The clean reads obtained were aligned to the genome sequence of E. coli O157:H7 EDL933 using SOAP2 PGCGROWTHCONDITIONS
The raw reads were filtered for removing dirty raw reads which contain adapters, unknown or low quality bases. PGCGROWTHCONDITIONS
The strain was stocked in tryptic soy broth (TSB) with 25% glycerol at -80℃, and was activated by streaking onto TSA plate and incubating at 37℃ for 24 h. And then, a single colony was picked and used to inoculate TSB and incubated at 37℃ for 12 h with shaking at 200 rpm. This overnight culture was transferred to TSB at a dilution of 1:100 and grew to the exponential phase (OD550=0.93). PGCGROWTHCONDITIONS
Total RNA was isolated from the VBNC cells and the exponential-phase cells using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. The RNA samples were treated with DNase Ⅰ (Invitrogen) to remove residual genomic DNA. PGCGROWTHCONDITIONS
treatment: None PGCGROWTHCONDITIONS
10 μg of total RNA sample was subjected to purification for discarding rRNA via the MICROBExpress kit (Ambion) according to the manufacturer’s protocol. Following purification, the RNA was interrupted into short fragments using divalent cations under elevated temperature and the short fragments were used for the cDNA synthesis using a SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) according to the manufacturer’s instructions. These cDNA fragments were purified with a QIAquick PCR purification kit (Qiagen), and then went through end reparation, adding poly(A) and ligation of sequencing adaptors. These products were purified with agarose gel electrophoresis and fragments in the size of 200-250 bp were selected for PCR amplification to construct the cDNA library. PGCGROWTHCONDITIONS
All those uniquely mapped reads were used to calculate the gene expression level by the RPKM method, which is able to eliminate the influence of different gene length and sequencing discrepancy on the calculation of gene expression and thus the calculated gene expression level can be directly used for comparing the difference of gene expression among samples. PGCGROWTHCONDITIONS
Bacterium PGCGROWTHCONDITIONS
Base calling performed using  Illumina GA pipeline 1.6. PGCGROWTHCONDITIONS
cas_RNAA PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: ASM666v1; NC_002655.2 PGCGROWTHCONDITIONS
In order to generate the VBNC state in E. coli O157:H7, 20 mL of the exponential-phase cell suspensions in a 50 mL sterile glass tube was treated by HPCD at 5 MPa and 25℃ for 40 min. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: O157:H7 NCTC 12900 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Microsoft excel spreadsheet files include RPKM values for each gene of sample PGCGROWTHCONDITIONS
The clean reads obtained were aligned to the genome sequence of E. coli O157:H7 EDL933 using SOAP2 PGCGROWTHCONDITIONS
The raw reads were filtered for removing dirty raw reads which contain adapters, unknown or low quality bases. PGCGROWTHCONDITIONS
The strain was stocked in tryptic soy broth (TSB) with 25% glycerol at -80℃, and was activated by streaking onto TSA plate and incubating at 37℃ for 24 h. And then, a single colony was picked and used to inoculate TSB and incubated at 37℃ for 12 h with shaking at 200 rpm. This overnight culture was transferred to TSB at a dilution of 1:100 and grew to the exponential phase (OD550=0.93). PGCGROWTHCONDITIONS
Total RNA was isolated from the VBNC cells and the exponential-phase cells using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. The RNA samples were treated with DNase Ⅰ (Invitrogen) to remove residual genomic DNA. PGCGROWTHCONDITIONS
treatment: Treated by HPCD at 5 MPa and 25℃ for 40 min PGCGROWTHCONDITIONS
Adapter cutting using cutadapt, version 1.2.1, parameters -e 0.1 -O 1 -m 12 PGCGROWTHCONDITIONS
E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: strain MG1655, version U00096.2, downloaded from NCBI PGCGROWTHCONDITIONS
Genome mapping using Bowtie, version 0.12.9, parameters for samples 1-5: -v 2 --best --strata -m 1, parameters for samples 6-9: -v 3 --best --strata -m 1 PGCGROWTHCONDITIONS
LB mRNA PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 10 PGCGROWTHCONDITIONS
Read counts were normalized by million mapped reads for each nucleotide PGCGROWTHCONDITIONS
Read using bedtools, version 2.17.0, parameter: -s, for samples 1-5 the middle nucleotide of each read was taken, for samples 6-9 the first nucleotide was taken and the read count was assigned to the nucleotide 5' of the first nucleotide see {Kertesz, 2010} for details PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-size selection and generation of the cDNA libraries was performed as described {Ingolia, 2009} PGCGROWTHCONDITIONS
strain: MC4100 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Column 1 names the nucleotide in the genome, column 2 gives counts for the forward strand, column 3 for the reverse strand, columns are tab separated PGCGROWTHCONDITIONS
Total RNA was extracted using TRIzol reagent (Invitrogen) and the sample was enriched in mRNA, depleting small RNAs with GeneJET™ RNA Purification Kit (Fermentas) and ribosomal RNA with two cycle of MICROBExpress™Bacterial mRNA Enrichment Kit (Ambion). To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95°C,refolded at 37 °C, after addition of 10x RNA-structure buffer with pH 7.0 (100 mM Tris, 1 M KCl, 100 mM MgCl2) and digested for 1 min at 37 °C with either 0.05 U RNase V1 (Life Technologies) or a combination of 2 µg RNase A and 5 U RNase T1 (Thermo Scientific). The reaction was stopped by extracting the RNA with phenol-chlorophorm. The RNase A/T1-digested sample was phosphorylated with T4 PNK (NEB) and purified with RNA Clean & Concentrator™ kit (Zymo Research). Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 (100 mM Na2CO3, 2 mM EDTA) for 12 min at 95°C. PGCGROWTHCONDITIONS
Adapter cutting using cutadapt, version 1.2.1, parameters -e 0.1 -O 1 -m 12 PGCGROWTHCONDITIONS
E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: strain MG1655, version U00096.2, downloaded from NCBI PGCGROWTHCONDITIONS
Genome mapping using Bowtie, version 0.12.9, parameters for samples 1-5: -v 2 --best --strata -m 1, parameters for samples 6-9: -v 3 --best --strata -m 1 PGCGROWTHCONDITIONS
LB RPF PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 10 PGCGROWTHCONDITIONS
Read counts were normalized by million mapped reads for each nucleotide PGCGROWTHCONDITIONS
Read using bedtools, version 2.17.0, parameter: -s, for samples 1-5 the middle nucleotide of each read was taken, for samples 6-9 the first nucleotide was taken and the read count was assigned to the nucleotide 5' of the first nucleotide see {Kertesz, 2010} for details PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-size selection and generation of the cDNA libraries was performed as described {Ingolia, 2009} PGCGROWTHCONDITIONS
sample type: ribosome protected PGCGROWTHCONDITIONS
strain: MC4100 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Column 1 names the nucleotide in the genome, column 2 gives counts for the forward strand, column 3 for the reverse strand, columns are tab separated PGCGROWTHCONDITIONS
Total RNA was extracted using TRIzol reagent (Invitrogen) and the sample was enriched in mRNA, depleting small RNAs with GeneJET™ RNA Purification Kit (Fermentas) and ribosomal RNA with two cycle of MICROBExpress™Bacterial mRNA Enrichment Kit (Ambion). To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95°C,refolded at 37 °C, after addition of 10x RNA-structure buffer with pH 7.0 (100 mM Tris, 1 M KCl, 100 mM MgCl2) and digested for 1 min at 37 °C with either 0.05 U RNase V1 (Life Technologies) or a combination of 2 µg RNase A and 5 U RNase T1 (Thermo Scientific). The reaction was stopped by extracting the RNA with phenol-chlorophorm. The RNase A/T1-digested sample was phosphorylated with T4 PNK (NEB) and purified with RNA Clean & Concentrator™ kit (Zymo Research). Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 (100 mM Na2CO3, 2 mM EDTA) for 12 min at 95°C. PGCGROWTHCONDITIONS
Adapter cutting using cutadapt, version 1.2.1, parameters -e 0.1 -O 1 -m 12 PGCGROWTHCONDITIONS
E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: strain MG1655, version U00096.2, downloaded from NCBI PGCGROWTHCONDITIONS
Genome mapping using Bowtie, version 0.12.9, parameters for samples 1-5: -v 2 --best --strata -m 1, parameters for samples 6-9: -v 3 --best --strata -m 1 PGCGROWTHCONDITIONS
LB mRNA technical replicate PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 10 PGCGROWTHCONDITIONS
Read counts were normalized by million mapped reads for each nucleotide PGCGROWTHCONDITIONS
Read using bedtools, version 2.17.0, parameter: -s, for samples 1-5 the middle nucleotide of each read was taken, for samples 6-9 the first nucleotide was taken and the read count was assigned to the nucleotide 5' of the first nucleotide see {Kertesz, 2010} for details PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-size selection and generation of the cDNA libraries was performed as described {Ingolia, 2009} PGCGROWTHCONDITIONS
strain: MC4101 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Column 1 names the nucleotide in the genome, column 2 gives counts for the forward strand, column 3 for the reverse strand, columns are tab separated PGCGROWTHCONDITIONS
Total RNA was extracted using TRIzol reagent (Invitrogen) and the sample was enriched in mRNA, depleting small RNAs with GeneJET™ RNA Purification Kit (Fermentas) and ribosomal RNA with two cycle of MICROBExpress™Bacterial mRNA Enrichment Kit (Ambion). To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95°C,refolded at 37 °C, after addition of 10x RNA-structure buffer with pH 7.0 (100 mM Tris, 1 M KCl, 100 mM MgCl2) and digested for 1 min at 37 °C with either 0.05 U RNase V1 (Life Technologies) or a combination of 2 µg RNase A and 5 U RNase T1 (Thermo Scientific). The reaction was stopped by extracting the RNA with phenol-chlorophorm. The RNase A/T1-digested sample was phosphorylated with T4 PNK (NEB) and purified with RNA Clean & Concentrator™ kit (Zymo Research). Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 (100 mM Na2CO3, 2 mM EDTA) for 12 min at 95°C. PGCGROWTHCONDITIONS
Adapter cutting using cutadapt, version 1.2.1, parameters -e 0.1 -O 1 -m 12 PGCGROWTHCONDITIONS
E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: strain MG1655, version U00096.2, downloaded from NCBI PGCGROWTHCONDITIONS
Genome mapping using Bowtie, version 0.12.9, parameters for samples 1-5: -v 2 --best --strata -m 1, parameters for samples 6-9: -v 3 --best --strata -m 1 PGCGROWTHCONDITIONS
LB RPF biological replicate PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 10 PGCGROWTHCONDITIONS
Read counts were normalized by million mapped reads for each nucleotide PGCGROWTHCONDITIONS
Read using bedtools, version 2.17.0, parameter: -s, for samples 1-5 the middle nucleotide of each read was taken, for samples 6-9 the first nucleotide was taken and the read count was assigned to the nucleotide 5' of the first nucleotide see {Kertesz, 2010} for details PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-size selection and generation of the cDNA libraries was performed as described {Ingolia, 2009} PGCGROWTHCONDITIONS
sample type: ribosome protected PGCGROWTHCONDITIONS
strain: MC4102 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Column 1 names the nucleotide in the genome, column 2 gives counts for the forward strand, column 3 for the reverse strand, columns are tab separated PGCGROWTHCONDITIONS
Total RNA was extracted using TRIzol reagent (Invitrogen) and the sample was enriched in mRNA, depleting small RNAs with GeneJET™ RNA Purification Kit (Fermentas) and ribosomal RNA with two cycle of MICROBExpress™Bacterial mRNA Enrichment Kit (Ambion). To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95°C,refolded at 37 °C, after addition of 10x RNA-structure buffer with pH 7.0 (100 mM Tris, 1 M KCl, 100 mM MgCl2) and digested for 1 min at 37 °C with either 0.05 U RNase V1 (Life Technologies) or a combination of 2 µg RNase A and 5 U RNase T1 (Thermo Scientific). The reaction was stopped by extracting the RNA with phenol-chlorophorm. The RNase A/T1-digested sample was phosphorylated with T4 PNK (NEB) and purified with RNA Clean & Concentrator™ kit (Zymo Research). Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 (100 mM Na2CO3, 2 mM EDTA) for 12 min at 95°C. PGCGROWTHCONDITIONS
Adapter cutting using cutadapt, version 1.2.1, parameters -e 0.1 -O 1 -m 12 PGCGROWTHCONDITIONS
E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: strain MG1655, version U00096.2, downloaded from NCBI PGCGROWTHCONDITIONS
Genome mapping using Bowtie, version 0.12.9, parameters for samples 1-5: -v 2 --best --strata -m 1, parameters for samples 6-9: -v 3 --best --strata -m 1 PGCGROWTHCONDITIONS
LB mRNA biological replicate PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 10 PGCGROWTHCONDITIONS
Read counts were normalized by million mapped reads for each nucleotide PGCGROWTHCONDITIONS
Read using bedtools, version 2.17.0, parameter: -s, for samples 1-5 the middle nucleotide of each read was taken, for samples 6-9 the first nucleotide was taken and the read count was assigned to the nucleotide 5' of the first nucleotide see {Kertesz, 2010} for details PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-size selection and generation of the cDNA libraries was performed as described {Ingolia, 2009} PGCGROWTHCONDITIONS
strain: MC4103 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Column 1 names the nucleotide in the genome, column 2 gives counts for the forward strand, column 3 for the reverse strand, columns are tab separated PGCGROWTHCONDITIONS
Total RNA was extracted using TRIzol reagent (Invitrogen) and the sample was enriched in mRNA, depleting small RNAs with GeneJET™ RNA Purification Kit (Fermentas) and ribosomal RNA with two cycle of MICROBExpress™Bacterial mRNA Enrichment Kit (Ambion). To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95°C,refolded at 37 °C, after addition of 10x RNA-structure buffer with pH 7.0 (100 mM Tris, 1 M KCl, 100 mM MgCl2) and digested for 1 min at 37 °C with either 0.05 U RNase V1 (Life Technologies) or a combination of 2 µg RNase A and 5 U RNase T1 (Thermo Scientific). The reaction was stopped by extracting the RNA with phenol-chlorophorm. The RNase A/T1-digested sample was phosphorylated with T4 PNK (NEB) and purified with RNA Clean & Concentrator™ kit (Zymo Research). Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 (100 mM Na2CO3, 2 mM EDTA) for 12 min at 95°C. PGCGROWTHCONDITIONS
Adapter cutting using cutadapt, version 1.2.1, parameters -e 0.1 -O 1 -m 12 PGCGROWTHCONDITIONS
E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: strain MG1655, version U00096.2, downloaded from NCBI PGCGROWTHCONDITIONS
Genome mapping using Bowtie, version 0.12.9, parameters for samples 1-5: -v 2 --best --strata -m 1, parameters for samples 6-9: -v 3 --best --strata -m 1 PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 10 PGCGROWTHCONDITIONS
Read counts were normalized by million mapped reads for each nucleotide PGCGROWTHCONDITIONS
Read using bedtools, version 2.17.0, parameter: -s, for samples 1-5 the middle nucleotide of each read was taken, for samples 6-9 the first nucleotide was taken and the read count was assigned to the nucleotide 5' of the first nucleotide see {Kertesz, 2010} for details PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-size selection and generation of the cDNA libraries was performed as described {Ingolia, 2009} PGCGROWTHCONDITIONS
sample type: V1 digested total RNA PGCGROWTHCONDITIONS
strain: MC4104 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Column 1 names the nucleotide in the genome, column 2 gives counts for the forward strand, column 3 for the reverse strand, columns are tab separated PGCGROWTHCONDITIONS
Total RNA was extracted using TRIzol reagent (Invitrogen) and the sample was enriched in mRNA, depleting small RNAs with GeneJET™ RNA Purification Kit (Fermentas) and ribosomal RNA with two cycle of MICROBExpress™Bacterial mRNA Enrichment Kit (Ambion). To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95°C,refolded at 37 °C, after addition of 10x RNA-structure buffer with pH 7.0 (100 mM Tris, 1 M KCl, 100 mM MgCl2) and digested for 1 min at 37 °C with either 0.05 U RNase V1 (Life Technologies) or a combination of 2 µg RNase A and 5 U RNase T1 (Thermo Scientific). The reaction was stopped by extracting the RNA with phenol-chlorophorm. The RNase A/T1-digested sample was phosphorylated with T4 PNK (NEB) and purified with RNA Clean & Concentrator™ kit (Zymo Research). Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 (100 mM Na2CO3, 2 mM EDTA) for 12 min at 95°C. PGCGROWTHCONDITIONS
V1 PGCGROWTHCONDITIONS
Adapter cutting using cutadapt, version 1.2.1, parameters -e 0.1 -O 1 -m 12 PGCGROWTHCONDITIONS
AT1 PGCGROWTHCONDITIONS
E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: strain MG1655, version U00096.2, downloaded from NCBI PGCGROWTHCONDITIONS
Genome mapping using Bowtie, version 0.12.9, parameters for samples 1-5: -v 2 --best --strata -m 1, parameters for samples 6-9: -v 3 --best --strata -m 1 PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 10 PGCGROWTHCONDITIONS
Read counts were normalized by million mapped reads for each nucleotide PGCGROWTHCONDITIONS
Read using bedtools, version 2.17.0, parameter: -s, for samples 1-5 the middle nucleotide of each read was taken, for samples 6-9 the first nucleotide was taken and the read count was assigned to the nucleotide 5' of the first nucleotide see {Kertesz, 2010} for details PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-size selection and generation of the cDNA libraries was performed as described {Ingolia, 2009} PGCGROWTHCONDITIONS
sample type: AT1 digested total RNA PGCGROWTHCONDITIONS
strain: MC4105 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Column 1 names the nucleotide in the genome, column 2 gives counts for the forward strand, column 3 for the reverse strand, columns are tab separated PGCGROWTHCONDITIONS
Total RNA was extracted using TRIzol reagent (Invitrogen) and the sample was enriched in mRNA, depleting small RNAs with GeneJET™ RNA Purification Kit (Fermentas) and ribosomal RNA with two cycle of MICROBExpress™Bacterial mRNA Enrichment Kit (Ambion). To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95°C,refolded at 37 °C, after addition of 10x RNA-structure buffer with pH 7.0 (100 mM Tris, 1 M KCl, 100 mM MgCl2) and digested for 1 min at 37 °C with either 0.05 U RNase V1 (Life Technologies) or a combination of 2 µg RNase A and 5 U RNase T1 (Thermo Scientific). The reaction was stopped by extracting the RNA with phenol-chlorophorm. The RNase A/T1-digested sample was phosphorylated with T4 PNK (NEB) and purified with RNA Clean & Concentrator™ kit (Zymo Research). Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 (100 mM Na2CO3, 2 mM EDTA) for 12 min at 95°C. PGCGROWTHCONDITIONS
Adapter cutting using cutadapt, version 1.2.1, parameters -e 0.1 -O 1 -m 12 PGCGROWTHCONDITIONS
E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: strain MG1655, version U00096.2, downloaded from NCBI PGCGROWTHCONDITIONS
Genome mapping using Bowtie, version 0.12.9, parameters for samples 1-5: -v 2 --best --strata -m 1, parameters for samples 6-9: -v 3 --best --strata -m 1 PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 10 PGCGROWTHCONDITIONS
Read counts were normalized by million mapped reads for each nucleotide PGCGROWTHCONDITIONS
Read using bedtools, version 2.17.0, parameter: -s, for samples 1-5 the middle nucleotide of each read was taken, for samples 6-9 the first nucleotide was taken and the read count was assigned to the nucleotide 5' of the first nucleotide see {Kertesz, 2010} for details PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-size selection and generation of the cDNA libraries was performed as described {Ingolia, 2009} PGCGROWTHCONDITIONS
sample type: V1 digested total RNA PGCGROWTHCONDITIONS
strain: MC4106 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Column 1 names the nucleotide in the genome, column 2 gives counts for the forward strand, column 3 for the reverse strand, columns are tab separated PGCGROWTHCONDITIONS
Total RNA was extracted using TRIzol reagent (Invitrogen) and the sample was enriched in mRNA, depleting small RNAs with GeneJET™ RNA Purification Kit (Fermentas) and ribosomal RNA with two cycle of MICROBExpress™Bacterial mRNA Enrichment Kit (Ambion). To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95°C,refolded at 37 °C, after addition of 10x RNA-structure buffer with pH 7.0 (100 mM Tris, 1 M KCl, 100 mM MgCl2) and digested for 1 min at 37 °C with either 0.05 U RNase V1 (Life Technologies) or a combination of 2 µg RNase A and 5 U RNase T1 (Thermo Scientific). The reaction was stopped by extracting the RNA with phenol-chlorophorm. The RNase A/T1-digested sample was phosphorylated with T4 PNK (NEB) and purified with RNA Clean & Concentrator™ kit (Zymo Research). Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 (100 mM Na2CO3, 2 mM EDTA) for 12 min at 95°C. PGCGROWTHCONDITIONS
V1 biological replicate PGCGROWTHCONDITIONS
Adapter cutting using cutadapt, version 1.2.1, parameters -e 0.1 -O 1 -m 12 PGCGROWTHCONDITIONS
AT1 biological replicate PGCGROWTHCONDITIONS
E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: strain MG1655, version U00096.2, downloaded from NCBI PGCGROWTHCONDITIONS
Genome mapping using Bowtie, version 0.12.9, parameters for samples 1-5: -v 2 --best --strata -m 1, parameters for samples 6-9: -v 3 --best --strata -m 1 PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 10 PGCGROWTHCONDITIONS
Read counts were normalized by million mapped reads for each nucleotide PGCGROWTHCONDITIONS
Read using bedtools, version 2.17.0, parameter: -s, for samples 1-5 the middle nucleotide of each read was taken, for samples 6-9 the first nucleotide was taken and the read count was assigned to the nucleotide 5' of the first nucleotide see {Kertesz, 2010} for details PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-size selection and generation of the cDNA libraries was performed as described {Ingolia, 2009} PGCGROWTHCONDITIONS
sample type: AT1 digested total RNA PGCGROWTHCONDITIONS
strain: MC4107 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Column 1 names the nucleotide in the genome, column 2 gives counts for the forward strand, column 3 for the reverse strand, columns are tab separated PGCGROWTHCONDITIONS
Total RNA was extracted using TRIzol reagent (Invitrogen) and the sample was enriched in mRNA, depleting small RNAs with GeneJET™ RNA Purification Kit (Fermentas) and ribosomal RNA with two cycle of MICROBExpress™Bacterial mRNA Enrichment Kit (Ambion). To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95°C,refolded at 37 °C, after addition of 10x RNA-structure buffer with pH 7.0 (100 mM Tris, 1 M KCl, 100 mM MgCl2) and digested for 1 min at 37 °C with either 0.05 U RNase V1 (Life Technologies) or a combination of 2 µg RNase A and 5 U RNase T1 (Thermo Scientific). The reaction was stopped by extracting the RNA with phenol-chlorophorm. The RNase A/T1-digested sample was phosphorylated with T4 PNK (NEB) and purified with RNA Clean & Concentrator™ kit (Zymo Research). Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 (100 mM Na2CO3, 2 mM EDTA) for 12 min at 95°C. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNAseq_delAr1_glycerol_NH4Cl_O2_1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: Crp_delAr1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNAseq_delAr1_glycerol_NH4Cl_O2_2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: Crp_delAr1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNAseq_delAr1_glycerol_NH4Cl_O2_3 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: Crp_delAr1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNAseq_delAr1delAr2_glycerol_NH4Cl_O2_1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: Crp_delAr1delAr2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNAseq_delAr1delAr2_glycerol_NH4Cl_O2_2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: Crp_delAr1delAr2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNAseq_delAr1delAr2_glycerol_NH4Cl_O2_3 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: Crp_delAr1delAr2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNAseq_delAr2_glycerol_NH4Cl_O2_1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: Crp_delAr2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNAseq_delAr2_glycerol_NH4Cl_O2_2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: Crp_delAr2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNAseq_delAr2_glycerol_NH4Cl_O2_3 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: Crp_delAr2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNAseq_delta-crp_fructose_NH4Cl_O2_1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: delta Crp PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNAseq_delta-crp_fructose_NH4Cl_O2_2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: delta Crp PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNAseq_delta-crp_fructose_NH4Cl_O2_3 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: delta Crp PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNAseq_delta-crp_glucose_NH4Cl_O2_1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: delta Crp PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNAseq_delta-crp_glucose_NH4Cl_O2_2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: delta Crp PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNAseq_delta-crp_glucose_NH4Cl_O2_3 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: delta Crp PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNAseq_delta-crp_glycerol_NH4Cl_O2_1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: delta Crp PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNAseq_delta-crp_glycerol_NH4Cl_O2_2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: delta Crp PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNAseq_delta-crp_glycerol_NH4Cl_O2_3 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: delta Crp PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNAseq_wt_fructose_NH4Cl_O2_1 PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: wt PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNAseq_wt_fructose_NH4Cl_O2_2 PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: wt PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNAseq_wt_glucose_NH4Cl_O2_1 PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: wt PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNAseq_wt_glucose_NH4Cl_O2_2 PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: wt PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNAseq_wt_glucose_NH4Cl_O2_3 PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: wt PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNAseq_wt_glycerol_NH4Cl_O2_1 PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: wt PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
E. coli K12 MG1655 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNAseq_wt_glycerol_NH4Cl_O2_2 PGCGROWTHCONDITIONS
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
strain: wt PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
Escherichia coli CSH50 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
GATC PGCGROWTHCONDITIONS
GATC software for read mapping on MG1655 PGCGROWTHCONDITIONS
gene expression sum normalized to 1 at each time point PGCGROWTHCONDITIONS
Gene wise natural spline interpolation of temporal data from initial time points to a dataset of 10 minutes steps (see processed data files). Expression values at the time points of the raw data are not affected by the interpolation. PGCGROWTHCONDITIONS
genotype: wildtype PGCGROWTHCONDITIONS
LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS
RNA extraction Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: CSH50 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression of genes in time, rows = genes, cols = time points PGCGROWTHCONDITIONS
time: 60 minutes PGCGROWTHCONDITIONS
verified with in-house pipeline PGCGROWTHCONDITIONS
Wt – 60 min PGCGROWTHCONDITIONS
Escherichia coli CSH50 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
GATC PGCGROWTHCONDITIONS
GATC software for read mapping on MG1655 PGCGROWTHCONDITIONS
gene expression sum normalized to 1 at each time point PGCGROWTHCONDITIONS
Gene wise natural spline interpolation of temporal data from initial time points to a dataset of 10 minutes steps (see processed data files). Expression values at the time points of the raw data are not affected by the interpolation. PGCGROWTHCONDITIONS
genotype: wildtype PGCGROWTHCONDITIONS
LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS
RNA extraction Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: CSH50 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression of genes in time, rows = genes, cols = time points PGCGROWTHCONDITIONS
time: 120 minutes PGCGROWTHCONDITIONS
verified with in-house pipeline PGCGROWTHCONDITIONS
Wt – 120 min PGCGROWTHCONDITIONS
Escherichia coli CSH50 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
GATC PGCGROWTHCONDITIONS
GATC software for read mapping on MG1655 PGCGROWTHCONDITIONS
gene expression sum normalized to 1 at each time point PGCGROWTHCONDITIONS
Gene wise natural spline interpolation of temporal data from initial time points to a dataset of 10 minutes steps (see processed data files). Expression values at the time points of the raw data are not affected by the interpolation. PGCGROWTHCONDITIONS
genotype: wildtype PGCGROWTHCONDITIONS
LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS
RNA extraction Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: CSH50 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression of genes in time, rows = genes, cols = time points PGCGROWTHCONDITIONS
time: 180 minutes PGCGROWTHCONDITIONS
verified with in-house pipeline PGCGROWTHCONDITIONS
Wt – 180 min PGCGROWTHCONDITIONS
Escherichia coli CSH50 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
GATC PGCGROWTHCONDITIONS
GATC software for read mapping on MG1655 PGCGROWTHCONDITIONS
gene expression sum normalized to 1 at each time point PGCGROWTHCONDITIONS
Gene wise natural spline interpolation of temporal data from initial time points to a dataset of 10 minutes steps (see processed data files). Expression values at the time points of the raw data are not affected by the interpolation. PGCGROWTHCONDITIONS
genotype: wildtype PGCGROWTHCONDITIONS
LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS
RNA extraction Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: CSH50 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression of genes in time, rows = genes, cols = time points PGCGROWTHCONDITIONS
time: 300 minutes PGCGROWTHCONDITIONS
verified with in-house pipeline PGCGROWTHCONDITIONS
Wt – 300 min PGCGROWTHCONDITIONS
Escherichia coli CSH50 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
GATC PGCGROWTHCONDITIONS
GATC software for read mapping on MG1655 PGCGROWTHCONDITIONS
gene expression sum normalized to 1 at each time point PGCGROWTHCONDITIONS
Gene wise natural spline interpolation of temporal data from initial time points to a dataset of 10 minutes steps (see processed data files). Expression values at the time points of the raw data are not affected by the interpolation. PGCGROWTHCONDITIONS
genotype: wildtype PGCGROWTHCONDITIONS
LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS
RNA extraction Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: CSH50 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression of genes in time, rows = genes, cols = time points PGCGROWTHCONDITIONS
time: 420 minutes PGCGROWTHCONDITIONS
verified with in-house pipeline PGCGROWTHCONDITIONS
Wt – 420 min PGCGROWTHCONDITIONS
Escherichia coli CSH50 Δfis PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Fis – 60 min PGCGROWTHCONDITIONS
GATC PGCGROWTHCONDITIONS
GATC software for read mapping on MG1655 PGCGROWTHCONDITIONS
gene expression sum normalized to 1 at each time point PGCGROWTHCONDITIONS
Gene wise natural spline interpolation of temporal data from initial time points to a dataset of 10 minutes steps (see processed data files). Expression values at the time points of the raw data are not affected by the interpolation. PGCGROWTHCONDITIONS
genotype: delta-fis PGCGROWTHCONDITIONS
LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS
RNA extraction Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: CSH50 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression of genes in time, rows = genes, cols = time points PGCGROWTHCONDITIONS
time: 60 minutes PGCGROWTHCONDITIONS
verified with in-house pipeline PGCGROWTHCONDITIONS
Escherichia coli CSH50 Δfis PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Fis – 120 min PGCGROWTHCONDITIONS
GATC PGCGROWTHCONDITIONS
GATC software for read mapping on MG1655 PGCGROWTHCONDITIONS
gene expression sum normalized to 1 at each time point PGCGROWTHCONDITIONS
Gene wise natural spline interpolation of temporal data from initial time points to a dataset of 10 minutes steps (see processed data files). Expression values at the time points of the raw data are not affected by the interpolation. PGCGROWTHCONDITIONS
genotype: delta-fis PGCGROWTHCONDITIONS
LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS
RNA extraction Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: CSH50 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression of genes in time, rows = genes, cols = time points PGCGROWTHCONDITIONS
time: 120 minutes PGCGROWTHCONDITIONS
verified with in-house pipeline PGCGROWTHCONDITIONS
Escherichia coli CSH50 Δfis PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Fis – 180 min PGCGROWTHCONDITIONS
GATC PGCGROWTHCONDITIONS
GATC software for read mapping on MG1655 PGCGROWTHCONDITIONS
gene expression sum normalized to 1 at each time point PGCGROWTHCONDITIONS
Gene wise natural spline interpolation of temporal data from initial time points to a dataset of 10 minutes steps (see processed data files). Expression values at the time points of the raw data are not affected by the interpolation. PGCGROWTHCONDITIONS
genotype: delta-fis PGCGROWTHCONDITIONS
LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS
RNA extraction Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: CSH50 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression of genes in time, rows = genes, cols = time points PGCGROWTHCONDITIONS
time: 180 minutes PGCGROWTHCONDITIONS
verified with in-house pipeline PGCGROWTHCONDITIONS
Escherichia coli CSH50 Δfis PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Fis – 420 min PGCGROWTHCONDITIONS
GATC PGCGROWTHCONDITIONS
GATC software for read mapping on MG1655 PGCGROWTHCONDITIONS
gene expression sum normalized to 1 at each time point PGCGROWTHCONDITIONS
Gene wise natural spline interpolation of temporal data from initial time points to a dataset of 10 minutes steps (see processed data files). Expression values at the time points of the raw data are not affected by the interpolation. PGCGROWTHCONDITIONS
genotype: delta-fis PGCGROWTHCONDITIONS
LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS
RNA extraction Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: CSH50 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression of genes in time, rows = genes, cols = time points PGCGROWTHCONDITIONS
time: 420 minutes PGCGROWTHCONDITIONS
verified with in-house pipeline PGCGROWTHCONDITIONS
Escherichia coli CSH50 Δhns PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
GATC PGCGROWTHCONDITIONS
GATC software for read mapping on MG1655 PGCGROWTHCONDITIONS
gene expression sum normalized to 1 at each time point PGCGROWTHCONDITIONS
Gene wise natural spline interpolation of temporal data from initial time points to a dataset of 10 minutes steps (see processed data files). Expression values at the time points of the raw data are not affected by the interpolation. PGCGROWTHCONDITIONS
genotype: delta-hns PGCGROWTHCONDITIONS
Hns – 60 min PGCGROWTHCONDITIONS
LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS
RNA extraction Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: CSH50 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression of genes in time, rows = genes, cols = time points PGCGROWTHCONDITIONS
time: 60 minutes PGCGROWTHCONDITIONS
verified with in-house pipeline PGCGROWTHCONDITIONS
Escherichia coli CSH50 Δhns PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
GATC PGCGROWTHCONDITIONS
GATC software for read mapping on MG1655 PGCGROWTHCONDITIONS
gene expression sum normalized to 1 at each time point PGCGROWTHCONDITIONS
Gene wise natural spline interpolation of temporal data from initial time points to a dataset of 10 minutes steps (see processed data files). Expression values at the time points of the raw data are not affected by the interpolation. PGCGROWTHCONDITIONS
genotype: delta-hns PGCGROWTHCONDITIONS
Hns – 120 min PGCGROWTHCONDITIONS
LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS
RNA extraction Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: CSH50 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression of genes in time, rows = genes, cols = time points PGCGROWTHCONDITIONS
time: 120 minutes PGCGROWTHCONDITIONS
verified with in-house pipeline PGCGROWTHCONDITIONS
Escherichia coli CSH50 Δhns PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
GATC PGCGROWTHCONDITIONS
GATC software for read mapping on MG1655 PGCGROWTHCONDITIONS
gene expression sum normalized to 1 at each time point PGCGROWTHCONDITIONS
Gene wise natural spline interpolation of temporal data from initial time points to a dataset of 10 minutes steps (see processed data files). Expression values at the time points of the raw data are not affected by the interpolation. PGCGROWTHCONDITIONS
genotype: delta-hns PGCGROWTHCONDITIONS
Hns -180 min PGCGROWTHCONDITIONS
LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS
RNA extraction Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: CSH50 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression of genes in time, rows = genes, cols = time points PGCGROWTHCONDITIONS
time: 180 minutes PGCGROWTHCONDITIONS
verified with in-house pipeline PGCGROWTHCONDITIONS
Escherichia coli CSH50 Δhns PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
GATC PGCGROWTHCONDITIONS
GATC software for read mapping on MG1655 PGCGROWTHCONDITIONS
gene expression sum normalized to 1 at each time point PGCGROWTHCONDITIONS
Gene wise natural spline interpolation of temporal data from initial time points to a dataset of 10 minutes steps (see processed data files). Expression values at the time points of the raw data are not affected by the interpolation. PGCGROWTHCONDITIONS
genotype: delta-hns PGCGROWTHCONDITIONS
Hns – 420 min PGCGROWTHCONDITIONS
LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS
RNA extraction Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: CSH50 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: expression of genes in time, rows = genes, cols = time points PGCGROWTHCONDITIONS
time: 420 minutes PGCGROWTHCONDITIONS
verified with in-house pipeline PGCGROWTHCONDITIONS
50 ng of the fragmented RNA was converted to sequencing library using TruSeq® Stranded mRNA Sample Prep Kit in accordance with manufacturer’s instruction (Illumina). PGCGROWTHCONDITIONS
All sequencing reads were mapped to E. coli MG1655 reference genome (NC_000913) using CLC Genomics Workbench5 with the length fraction of 0.9 and the similarity of 0.99. PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.4 PGCGROWTHCONDITIONS
cell type: Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
From the cells cultured in LB media at 37 ℃, total RNA was extracted using RNAsnapTM method, followed by the ethanol precipitation. rRNA was removed using ribo-zeroTM magnetic kit for bacteria in accordance with manufacturer’s instruction (Epicentre). rRNA removal was confirmed using ExperionTM system. Subsequently, 4 µg of the purified RNA was fragmented to sizes of ~300 bp using RNA fragmentation reagent (Ambion, Grand Island, NY). PGCGROWTHCONDITIONS
Glycerol stocks of E. coli K12 strain MG1655 were inoculated into LB media  grown at 37 ℃ with constant agitation overnight. Cultures were diluted 1:100 into fresh minimal medium and then cultured at 37 ℃ to mid-exponential phase (OD600 nm ~ 0.6). PGCGROWTHCONDITIONS
No treatment PGCGROWTHCONDITIONS
RNA-seq 37C LB rep1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPKM is generated by in-house script PGCGROWTHCONDITIONS
The expression levels were based upon the RPKM metric obtained from strand-specific manner. PGCGROWTHCONDITIONS
50 ng of the fragmented RNA was converted to sequencing library using TruSeq® Stranded mRNA Sample Prep Kit in accordance with manufacturer’s instruction (Illumina). PGCGROWTHCONDITIONS
All sequencing reads were mapped to E. coli MG1655 reference genome (NC_000913) using CLC Genomics Workbench5 with the length fraction of 0.9 and the similarity of 0.99. PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.4 PGCGROWTHCONDITIONS
cell type: Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
From the cells cultured in LB media at 37 ℃, total RNA was extracted using RNAsnapTM method, followed by the ethanol precipitation. rRNA was removed using ribo-zeroTM magnetic kit for bacteria in accordance with manufacturer’s instruction (Epicentre). rRNA removal was confirmed using ExperionTM system. Subsequently, 4 µg of the purified RNA was fragmented to sizes of ~300 bp using RNA fragmentation reagent (Ambion, Grand Island, NY). PGCGROWTHCONDITIONS
Glycerol stocks of E. coli K12 strain MG1655 were inoculated into LB media  grown at 37 ℃ with constant agitation overnight. Cultures were diluted 1:100 into fresh minimal medium and then cultured at 37 ℃ to mid-exponential phase (OD600 nm ~ 0.6). PGCGROWTHCONDITIONS
No treatment PGCGROWTHCONDITIONS
RNA-seq 37C LB rep2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPKM is generated by in-house script PGCGROWTHCONDITIONS
The expression levels were based upon the RPKM metric obtained from strand-specific manner. PGCGROWTHCONDITIONS
Escherichia coli B strain REL606 was revived from a freezer stock via overnight growth in 10 ml Davis Minimal medium supplemented with limiting glucose at 0.5 g/l (DM500) in a 50 ml Erlenmeyer flask. This culture was diluted 100-fold into 50 ml fresh DM500 in a 250 ml Erlenmeyer flask and incubated for 24 hours. To initiate the experiment, these preconditioned cultures were diluted 100-fold into 50 ml fresh DM500 in multiple 250 ml Erlenmeyer flasks and grown for the specified times until harvesting cells for total RNA isolation. All growth steps were conducted with incubation at 37°C and orbital shaking at 120 r.p.m. over a one-inch diameter. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Exact details for the full computational pipeline are available at https://github.com/wilkelab/AG3C_starvation_tc_RNAseq. PGCGROWTHCONDITIONS
Genome_build: NC_012967.1 plus small RNAs as annotated in Rfam 11.0 database PGCGROWTHCONDITIONS
Glucose time course, 5 hour time point, biological replicate 1 PGCGROWTHCONDITIONS
Mapped R1 reads in single-end mode using Bowtie2 2.1.0 with the –k 1 option PGCGROWTHCONDITIONS
molecule subtype: rRNA-depleted total RNA PGCGROWTHCONDITIONS
REL606_glucose-limited minimal medium_5 hr PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNAsnap followed by RiboZero rRNA removal kit for gram-negative bacteria (Epicentre) PGCGROWTHCONDITIONS
RNA was fragmented using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). Then, RNA was phosphorylated using T4 polynucleotide kinase and prepared using the NEBNext Small RNA Library Prep Set for Illumina (Multiplex Compatible). DNA fragments greater than 100 bp were excised from a 4% agarose gel after library preparation and recovered using the Zymoclean Gel DNA Recovery Kit (Zymo Research). PGCGROWTHCONDITIONS
strain: REL606 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Read counts aligned to genes and noncoding Rfam features in CSV format PGCGROWTHCONDITIONS
The number of R1 reads mapping to each gene were counted using HTSeq 0.6.0 PGCGROWTHCONDITIONS
time point: 5 hours PGCGROWTHCONDITIONS
Trimmed adaptor sequences from reads using Flexbar 2.31 PGCGROWTHCONDITIONS
Escherichia coli B strain REL606 was revived from a freezer stock via overnight growth in 10 ml Davis Minimal medium supplemented with limiting glucose at 0.5 g/l (DM500) in a 50 ml Erlenmeyer flask. This culture was diluted 100-fold into 50 ml fresh DM500 in a 250 ml Erlenmeyer flask and incubated for 24 hours. To initiate the experiment, these preconditioned cultures were diluted 100-fold into 50 ml fresh DM500 in multiple 250 ml Erlenmeyer flasks and grown for the specified times until harvesting cells for total RNA isolation. All growth steps were conducted with incubation at 37°C and orbital shaking at 120 r.p.m. over a one-inch diameter. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Exact details for the full computational pipeline are available at https://github.com/wilkelab/AG3C_starvation_tc_RNAseq. PGCGROWTHCONDITIONS
Genome_build: NC_012967.1 plus small RNAs as annotated in Rfam 11.0 database PGCGROWTHCONDITIONS
Glucose time course, 168 hour time point, biological replicate 3 PGCGROWTHCONDITIONS
Mapped R1 reads in single-end mode using Bowtie2 2.1.0 with the –k 1 option PGCGROWTHCONDITIONS
molecule subtype: rRNA-depleted total RNA PGCGROWTHCONDITIONS
REL606_glucose-limited minimal medium_168 hr PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNAsnap followed by RiboZero rRNA removal kit for gram-negative bacteria (Epicentre) PGCGROWTHCONDITIONS
RNA was fragmented using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). Then, RNA was phosphorylated using T4 polynucleotide kinase and prepared using the NEBNext Small RNA Library Prep Set for Illumina (Multiplex Compatible). DNA fragments greater than 100 bp were excised from a 4% agarose gel after library preparation and recovered using the Zymoclean Gel DNA Recovery Kit (Zymo Research). PGCGROWTHCONDITIONS
strain: REL606 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Read counts aligned to genes and noncoding Rfam features in CSV format PGCGROWTHCONDITIONS
The number of R1 reads mapping to each gene were counted using HTSeq 0.6.0 PGCGROWTHCONDITIONS
time point: 168 hours PGCGROWTHCONDITIONS
Trimmed adaptor sequences from reads using Flexbar 2.31 PGCGROWTHCONDITIONS
Escherichia coli B strain REL606 was revived from a freezer stock via overnight growth in 10 ml Davis Minimal medium supplemented with limiting glucose at 0.5 g/l (DM500) in a 50 ml Erlenmeyer flask. This culture was diluted 100-fold into 50 ml fresh DM500 in a 250 ml Erlenmeyer flask and incubated for 24 hours. To initiate the experiment, these preconditioned cultures were diluted 100-fold into 50 ml fresh DM500 in multiple 250 ml Erlenmeyer flasks and grown for the specified times until harvesting cells for total RNA isolation. All growth steps were conducted with incubation at 37°C and orbital shaking at 120 r.p.m. over a one-inch diameter. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Exact details for the full computational pipeline are available at https://github.com/wilkelab/AG3C_starvation_tc_RNAseq. PGCGROWTHCONDITIONS
Genome_build: NC_012967.1 plus small RNAs as annotated in Rfam 11.0 database PGCGROWTHCONDITIONS
Glucose time course, 336 hour time point, biological replicate 3 PGCGROWTHCONDITIONS
Mapped R1 reads in single-end mode using Bowtie2 2.1.0 with the –k 1 option PGCGROWTHCONDITIONS
molecule subtype: rRNA-depleted total RNA PGCGROWTHCONDITIONS
REL606_glucose-limited minimal medium_336 hr PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNAsnap followed by RiboZero rRNA removal kit for gram-negative bacteria (Epicentre) PGCGROWTHCONDITIONS
RNA was fragmented using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). Then, RNA was phosphorylated using T4 polynucleotide kinase and prepared using the NEBNext Small RNA Library Prep Set for Illumina (Multiplex Compatible). DNA fragments greater than 100 bp were excised from a 4% agarose gel after library preparation and recovered using the Zymoclean Gel DNA Recovery Kit (Zymo Research). PGCGROWTHCONDITIONS
strain: REL606 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Read counts aligned to genes and noncoding Rfam features in CSV format PGCGROWTHCONDITIONS
The number of R1 reads mapping to each gene were counted using HTSeq 0.6.0 PGCGROWTHCONDITIONS
time point: 336 hours PGCGROWTHCONDITIONS
Trimmed adaptor sequences from reads using Flexbar 2.31 PGCGROWTHCONDITIONS
Escherichia coli B strain REL606 was revived from a freezer stock via overnight growth in 10 ml Davis Minimal medium supplemented with limiting glucose at 0.5 g/l (DM500) in a 50 ml Erlenmeyer flask. This culture was diluted 100-fold into 50 ml fresh DM500 in a 250 ml Erlenmeyer flask and incubated for 24 hours. To initiate the experiment, these preconditioned cultures were diluted 100-fold into 50 ml fresh DM500 in multiple 250 ml Erlenmeyer flasks and grown for the specified times until harvesting cells for total RNA isolation. All growth steps were conducted with incubation at 37°C and orbital shaking at 120 r.p.m. over a one-inch diameter. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Exact details for the full computational pipeline are available at https://github.com/wilkelab/AG3C_starvation_tc_RNAseq. PGCGROWTHCONDITIONS
Genome_build: NC_012967.1 plus small RNAs as annotated in Rfam 11.0 database PGCGROWTHCONDITIONS
Glucose time course, 3 hour time point, biological replicate 3, rRNA not depleted PGCGROWTHCONDITIONS
Mapped R1 reads in single-end mode using Bowtie2 2.1.0 with the –k 1 option PGCGROWTHCONDITIONS
molecule subtype: total RNA PGCGROWTHCONDITIONS
REL606_glucose-limited minimal medium_3 hr_rRNA not depleted PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNAsnap PGCGROWTHCONDITIONS
RNA was fragmented using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). Then, RNA was phosphorylated using T4 polynucleotide kinase and prepared using the NEBNext Small RNA Library Prep Set for Illumina (Multiplex Compatible). DNA fragments greater than 100 bp were excised from a 4% agarose gel after library preparation and recovered using the Zymoclean Gel DNA Recovery Kit (Zymo Research). PGCGROWTHCONDITIONS
strain: REL606 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Read counts aligned to genes and noncoding Rfam features in CSV format PGCGROWTHCONDITIONS
The number of R1 reads mapping to each gene were counted using HTSeq 0.6.0 PGCGROWTHCONDITIONS
time point: 3 hours PGCGROWTHCONDITIONS
Trimmed adaptor sequences from reads using Flexbar 2.31 PGCGROWTHCONDITIONS
Escherichia coli B strain REL606 was revived from a freezer stock via overnight growth in 10 ml Davis Minimal medium supplemented with limiting glucose at 0.5 g/l (DM500) in a 50 ml Erlenmeyer flask. This culture was diluted 100-fold into 50 ml fresh DM500 in a 250 ml Erlenmeyer flask and incubated for 24 hours. To initiate the experiment, these preconditioned cultures were diluted 100-fold into 50 ml fresh DM500 in multiple 250 ml Erlenmeyer flasks and grown for the specified times until harvesting cells for total RNA isolation. All growth steps were conducted with incubation at 37°C and orbital shaking at 120 r.p.m. over a one-inch diameter. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Exact details for the full computational pipeline are available at https://github.com/wilkelab/AG3C_starvation_tc_RNAseq. PGCGROWTHCONDITIONS
Genome_build: NC_012967.1 plus small RNAs as annotated in Rfam 11.0 database PGCGROWTHCONDITIONS
Glucose time course, 4 hour time point, biological replicate 3, rRNA not depleted PGCGROWTHCONDITIONS
Mapped R1 reads in single-end mode using Bowtie2 2.1.0 with the –k 1 option PGCGROWTHCONDITIONS
molecule subtype: total RNA PGCGROWTHCONDITIONS
REL606_glucose-limited minimal medium_4 hr_rRNA not depleted PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNAsnap PGCGROWTHCONDITIONS
RNA was fragmented using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). Then, RNA was phosphorylated using T4 polynucleotide kinase and prepared using the NEBNext Small RNA Library Prep Set for Illumina (Multiplex Compatible). DNA fragments greater than 100 bp were excised from a 4% agarose gel after library preparation and recovered using the Zymoclean Gel DNA Recovery Kit (Zymo Research). PGCGROWTHCONDITIONS
strain: REL606 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Read counts aligned to genes and noncoding Rfam features in CSV format PGCGROWTHCONDITIONS
The number of R1 reads mapping to each gene were counted using HTSeq 0.6.0 PGCGROWTHCONDITIONS
time point: 4 hours PGCGROWTHCONDITIONS
Trimmed adaptor sequences from reads using Flexbar 2.31 PGCGROWTHCONDITIONS
Aeration was initiated at 1 l/min when the culture reached an OD (600nm) of 3. PGCGROWTHCONDITIONS
alignment: STAR 2.4.0i PGCGROWTHCONDITIONS
batch culture rep1, 0 min PGCGROWTHCONDITIONS
batch culture PGCGROWTHCONDITIONS
Cell were grown in 3-liter stirred tank bioreactor anaerobically. The growth medium contained Na2H2PO4 (1.1 g/l), K2HPO4 (2.5 g/l), (NH4)2SO4 (9.0 g/l), Glucose (15.0 g/l), CaCl2 (2.2 mg/l), MgSO4 (0.55 g/l), NaH2-Citrate (234 mg/l), FeCl3*6 H2O (25.0 mg/l), ZnSO4*7 H2O (0.18 mg/l), MnSO4*7 H2O (0.1 mg/l), CuSO4*5 H2O (0.16 mg/l), CoCl2*6 H2O (0.18 mg/l). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
gene counting: HTSeq-Count 0.6.0 PGCGROWTHCONDITIONS
Genome_build: NC007779.1 (UCSC Archaeal Genome Browser) PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were treated with RNAprotect (Qiagen, Hilden, Germany) and stored at -80°C until preparation. rRNA was removed using RiboZero rRNA Removal Kit (Illumina, San Diego, CA), and sequencing libraries were prepared with TruSeq™ RNA Sample Preparation Kitv2 (Illumina) PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The file format is .xlsx. The file contains the raw gene counts of all samples. PGCGROWTHCONDITIONS
time: 0 min PGCGROWTHCONDITIONS
Aeration was initiated at 1 l/min when the culture reached an OD (600nm) of 3. PGCGROWTHCONDITIONS
alignment: STAR 2.4.0i PGCGROWTHCONDITIONS
batch culture rep1, 0.5 min PGCGROWTHCONDITIONS
batch culture PGCGROWTHCONDITIONS
Cell were grown in 3-liter stirred tank bioreactor anaerobically. The growth medium contained Na2H2PO4 (1.1 g/l), K2HPO4 (2.5 g/l), (NH4)2SO4 (9.0 g/l), Glucose (15.0 g/l), CaCl2 (2.2 mg/l), MgSO4 (0.55 g/l), NaH2-Citrate (234 mg/l), FeCl3*6 H2O (25.0 mg/l), ZnSO4*7 H2O (0.18 mg/l), MnSO4*7 H2O (0.1 mg/l), CuSO4*5 H2O (0.16 mg/l), CoCl2*6 H2O (0.18 mg/l). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
gene counting: HTSeq-Count 0.6.0 PGCGROWTHCONDITIONS
Genome_build: NC007779.1 (UCSC Archaeal Genome Browser) PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were treated with RNAprotect (Qiagen, Hilden, Germany) and stored at -80°C until preparation. rRNA was removed using RiboZero rRNA Removal Kit (Illumina, San Diego, CA), and sequencing libraries were prepared with TruSeq™ RNA Sample Preparation Kitv2 (Illumina) PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The file format is .xlsx. The file contains the raw gene counts of all samples. PGCGROWTHCONDITIONS
time: 0.5 min PGCGROWTHCONDITIONS
Aeration was initiated at 1 l/min when the culture reached an OD (600nm) of 3. PGCGROWTHCONDITIONS
alignment: STAR 2.4.0i PGCGROWTHCONDITIONS
batch culture rep1, 1 min PGCGROWTHCONDITIONS
batch culture PGCGROWTHCONDITIONS
Cell were grown in 3-liter stirred tank bioreactor anaerobically. The growth medium contained Na2H2PO4 (1.1 g/l), K2HPO4 (2.5 g/l), (NH4)2SO4 (9.0 g/l), Glucose (15.0 g/l), CaCl2 (2.2 mg/l), MgSO4 (0.55 g/l), NaH2-Citrate (234 mg/l), FeCl3*6 H2O (25.0 mg/l), ZnSO4*7 H2O (0.18 mg/l), MnSO4*7 H2O (0.1 mg/l), CuSO4*5 H2O (0.16 mg/l), CoCl2*6 H2O (0.18 mg/l). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
gene counting: HTSeq-Count 0.6.0 PGCGROWTHCONDITIONS
Genome_build: NC007779.1 (UCSC Archaeal Genome Browser) PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were treated with RNAprotect (Qiagen, Hilden, Germany) and stored at -80°C until preparation. rRNA was removed using RiboZero rRNA Removal Kit (Illumina, San Diego, CA), and sequencing libraries were prepared with TruSeq™ RNA Sample Preparation Kitv2 (Illumina) PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The file format is .xlsx. The file contains the raw gene counts of all samples. PGCGROWTHCONDITIONS
time: 1 min PGCGROWTHCONDITIONS
Aeration was initiated at 1 l/min when the culture reached an OD (600nm) of 3. PGCGROWTHCONDITIONS
alignment: STAR 2.4.0i PGCGROWTHCONDITIONS
batch culture rep1, 2 min PGCGROWTHCONDITIONS
batch culture PGCGROWTHCONDITIONS
Cell were grown in 3-liter stirred tank bioreactor anaerobically. The growth medium contained Na2H2PO4 (1.1 g/l), K2HPO4 (2.5 g/l), (NH4)2SO4 (9.0 g/l), Glucose (15.0 g/l), CaCl2 (2.2 mg/l), MgSO4 (0.55 g/l), NaH2-Citrate (234 mg/l), FeCl3*6 H2O (25.0 mg/l), ZnSO4*7 H2O (0.18 mg/l), MnSO4*7 H2O (0.1 mg/l), CuSO4*5 H2O (0.16 mg/l), CoCl2*6 H2O (0.18 mg/l). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
gene counting: HTSeq-Count 0.6.0 PGCGROWTHCONDITIONS
Genome_build: NC007779.1 (UCSC Archaeal Genome Browser) PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were treated with RNAprotect (Qiagen, Hilden, Germany) and stored at -80°C until preparation. rRNA was removed using RiboZero rRNA Removal Kit (Illumina, San Diego, CA), and sequencing libraries were prepared with TruSeq™ RNA Sample Preparation Kitv2 (Illumina) PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The file format is .xlsx. The file contains the raw gene counts of all samples. PGCGROWTHCONDITIONS
time: 2 min PGCGROWTHCONDITIONS
Aeration was initiated at 1 l/min when the culture reached an OD (600nm) of 3. PGCGROWTHCONDITIONS
alignment: STAR 2.4.0i PGCGROWTHCONDITIONS
batch culture rep1, 5 min PGCGROWTHCONDITIONS
batch culture PGCGROWTHCONDITIONS
Cell were grown in 3-liter stirred tank bioreactor anaerobically. The growth medium contained Na2H2PO4 (1.1 g/l), K2HPO4 (2.5 g/l), (NH4)2SO4 (9.0 g/l), Glucose (15.0 g/l), CaCl2 (2.2 mg/l), MgSO4 (0.55 g/l), NaH2-Citrate (234 mg/l), FeCl3*6 H2O (25.0 mg/l), ZnSO4*7 H2O (0.18 mg/l), MnSO4*7 H2O (0.1 mg/l), CuSO4*5 H2O (0.16 mg/l), CoCl2*6 H2O (0.18 mg/l). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
gene counting: HTSeq-Count 0.6.0 PGCGROWTHCONDITIONS
Genome_build: NC007779.1 (UCSC Archaeal Genome Browser) PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were treated with RNAprotect (Qiagen, Hilden, Germany) and stored at -80°C until preparation. rRNA was removed using RiboZero rRNA Removal Kit (Illumina, San Diego, CA), and sequencing libraries were prepared with TruSeq™ RNA Sample Preparation Kitv2 (Illumina) PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The file format is .xlsx. The file contains the raw gene counts of all samples. PGCGROWTHCONDITIONS
time: 5 min PGCGROWTHCONDITIONS
Aeration was initiated at 1 l/min when the culture reached an OD (600nm) of 3. PGCGROWTHCONDITIONS
alignment: STAR 2.4.0i PGCGROWTHCONDITIONS
batch culture rep1, 10 min PGCGROWTHCONDITIONS
batch culture PGCGROWTHCONDITIONS
Cell were grown in 3-liter stirred tank bioreactor anaerobically. The growth medium contained Na2H2PO4 (1.1 g/l), K2HPO4 (2.5 g/l), (NH4)2SO4 (9.0 g/l), Glucose (15.0 g/l), CaCl2 (2.2 mg/l), MgSO4 (0.55 g/l), NaH2-Citrate (234 mg/l), FeCl3*6 H2O (25.0 mg/l), ZnSO4*7 H2O (0.18 mg/l), MnSO4*7 H2O (0.1 mg/l), CuSO4*5 H2O (0.16 mg/l), CoCl2*6 H2O (0.18 mg/l). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
gene counting: HTSeq-Count 0.6.0 PGCGROWTHCONDITIONS
Genome_build: NC007779.1 (UCSC Archaeal Genome Browser) PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were treated with RNAprotect (Qiagen, Hilden, Germany) and stored at -80°C until preparation. rRNA was removed using RiboZero rRNA Removal Kit (Illumina, San Diego, CA), and sequencing libraries were prepared with TruSeq™ RNA Sample Preparation Kitv2 (Illumina) PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The file format is .xlsx. The file contains the raw gene counts of all samples. PGCGROWTHCONDITIONS
time: 10 min PGCGROWTHCONDITIONS
Aeration was initiated at 1 l/min when the culture reached an OD (600nm) of 3. PGCGROWTHCONDITIONS
alignment: STAR 2.4.0i PGCGROWTHCONDITIONS
batch culture rep2, 0 min PGCGROWTHCONDITIONS
batch culture PGCGROWTHCONDITIONS
Cell were grown in 3-liter stirred tank bioreactor anaerobically. The growth medium contained Na2H2PO4 (1.1 g/l), K2HPO4 (2.5 g/l), (NH4)2SO4 (9.0 g/l), Glucose (15.0 g/l), CaCl2 (2.2 mg/l), MgSO4 (0.55 g/l), NaH2-Citrate (234 mg/l), FeCl3*6 H2O (25.0 mg/l), ZnSO4*7 H2O (0.18 mg/l), MnSO4*7 H2O (0.1 mg/l), CuSO4*5 H2O (0.16 mg/l), CoCl2*6 H2O (0.18 mg/l). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
gene counting: HTSeq-Count 0.6.0 PGCGROWTHCONDITIONS
Genome_build: NC007779.1 (UCSC Archaeal Genome Browser) PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were treated with RNAprotect (Qiagen, Hilden, Germany) and stored at -80°C until preparation. rRNA was removed using RiboZero rRNA Removal Kit (Illumina, San Diego, CA), and sequencing libraries were prepared with TruSeq™ RNA Sample Preparation Kitv2 (Illumina) PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The file format is .xlsx. The file contains the raw gene counts of all samples. PGCGROWTHCONDITIONS
time: 0 min PGCGROWTHCONDITIONS
Aeration was initiated at 1 l/min when the culture reached an OD (600nm) of 3. PGCGROWTHCONDITIONS
alignment: STAR 2.4.0i PGCGROWTHCONDITIONS
batch culture rep2, 0.5 min PGCGROWTHCONDITIONS
batch culture PGCGROWTHCONDITIONS
Cell were grown in 3-liter stirred tank bioreactor anaerobically. The growth medium contained Na2H2PO4 (1.1 g/l), K2HPO4 (2.5 g/l), (NH4)2SO4 (9.0 g/l), Glucose (15.0 g/l), CaCl2 (2.2 mg/l), MgSO4 (0.55 g/l), NaH2-Citrate (234 mg/l), FeCl3*6 H2O (25.0 mg/l), ZnSO4*7 H2O (0.18 mg/l), MnSO4*7 H2O (0.1 mg/l), CuSO4*5 H2O (0.16 mg/l), CoCl2*6 H2O (0.18 mg/l). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
gene counting: HTSeq-Count 0.6.0 PGCGROWTHCONDITIONS
Genome_build: NC007779.1 (UCSC Archaeal Genome Browser) PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were treated with RNAprotect (Qiagen, Hilden, Germany) and stored at -80°C until preparation. rRNA was removed using RiboZero rRNA Removal Kit (Illumina, San Diego, CA), and sequencing libraries were prepared with TruSeq™ RNA Sample Preparation Kitv2 (Illumina) PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The file format is .xlsx. The file contains the raw gene counts of all samples. PGCGROWTHCONDITIONS
time: 0.5 min PGCGROWTHCONDITIONS
Aeration was initiated at 1 l/min when the culture reached an OD (600nm) of 3. PGCGROWTHCONDITIONS
alignment: STAR 2.4.0i PGCGROWTHCONDITIONS
batch culture rep2, 1 min PGCGROWTHCONDITIONS
batch culture PGCGROWTHCONDITIONS
Cell were grown in 3-liter stirred tank bioreactor anaerobically. The growth medium contained Na2H2PO4 (1.1 g/l), K2HPO4 (2.5 g/l), (NH4)2SO4 (9.0 g/l), Glucose (15.0 g/l), CaCl2 (2.2 mg/l), MgSO4 (0.55 g/l), NaH2-Citrate (234 mg/l), FeCl3*6 H2O (25.0 mg/l), ZnSO4*7 H2O (0.18 mg/l), MnSO4*7 H2O (0.1 mg/l), CuSO4*5 H2O (0.16 mg/l), CoCl2*6 H2O (0.18 mg/l). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
gene counting: HTSeq-Count 0.6.0 PGCGROWTHCONDITIONS
Genome_build: NC007779.1 (UCSC Archaeal Genome Browser) PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were treated with RNAprotect (Qiagen, Hilden, Germany) and stored at -80°C until preparation. rRNA was removed using RiboZero rRNA Removal Kit (Illumina, San Diego, CA), and sequencing libraries were prepared with TruSeq™ RNA Sample Preparation Kitv2 (Illumina) PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The file format is .xlsx. The file contains the raw gene counts of all samples. PGCGROWTHCONDITIONS
time: 1 min PGCGROWTHCONDITIONS
Aeration was initiated at 1 l/min when the culture reached an OD (600nm) of 3. PGCGROWTHCONDITIONS
alignment: STAR 2.4.0i PGCGROWTHCONDITIONS
batch culture rep2, 2 min PGCGROWTHCONDITIONS
batch culture PGCGROWTHCONDITIONS
Cell were grown in 3-liter stirred tank bioreactor anaerobically. The growth medium contained Na2H2PO4 (1.1 g/l), K2HPO4 (2.5 g/l), (NH4)2SO4 (9.0 g/l), Glucose (15.0 g/l), CaCl2 (2.2 mg/l), MgSO4 (0.55 g/l), NaH2-Citrate (234 mg/l), FeCl3*6 H2O (25.0 mg/l), ZnSO4*7 H2O (0.18 mg/l), MnSO4*7 H2O (0.1 mg/l), CuSO4*5 H2O (0.16 mg/l), CoCl2*6 H2O (0.18 mg/l). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
gene counting: HTSeq-Count 0.6.0 PGCGROWTHCONDITIONS
Genome_build: NC007779.1 (UCSC Archaeal Genome Browser) PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were treated with RNAprotect (Qiagen, Hilden, Germany) and stored at -80°C until preparation. rRNA was removed using RiboZero rRNA Removal Kit (Illumina, San Diego, CA), and sequencing libraries were prepared with TruSeq™ RNA Sample Preparation Kitv2 (Illumina) PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The file format is .xlsx. The file contains the raw gene counts of all samples. PGCGROWTHCONDITIONS
time: 2 min PGCGROWTHCONDITIONS
Aeration was initiated at 1 l/min when the culture reached an OD (600nm) of 3. PGCGROWTHCONDITIONS
alignment: STAR 2.4.0i PGCGROWTHCONDITIONS
batch culture rep2, 5 min PGCGROWTHCONDITIONS
batch culture PGCGROWTHCONDITIONS
Cell were grown in 3-liter stirred tank bioreactor anaerobically. The growth medium contained Na2H2PO4 (1.1 g/l), K2HPO4 (2.5 g/l), (NH4)2SO4 (9.0 g/l), Glucose (15.0 g/l), CaCl2 (2.2 mg/l), MgSO4 (0.55 g/l), NaH2-Citrate (234 mg/l), FeCl3*6 H2O (25.0 mg/l), ZnSO4*7 H2O (0.18 mg/l), MnSO4*7 H2O (0.1 mg/l), CuSO4*5 H2O (0.16 mg/l), CoCl2*6 H2O (0.18 mg/l). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
gene counting: HTSeq-Count 0.6.0 PGCGROWTHCONDITIONS
Genome_build: NC007779.1 (UCSC Archaeal Genome Browser) PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were treated with RNAprotect (Qiagen, Hilden, Germany) and stored at -80°C until preparation. rRNA was removed using RiboZero rRNA Removal Kit (Illumina, San Diego, CA), and sequencing libraries were prepared with TruSeq™ RNA Sample Preparation Kitv2 (Illumina) PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The file format is .xlsx. The file contains the raw gene counts of all samples. PGCGROWTHCONDITIONS
time: 5 min PGCGROWTHCONDITIONS
Aeration was initiated at 1 l/min when the culture reached an OD (600nm) of 3. PGCGROWTHCONDITIONS
alignment: STAR 2.4.0i PGCGROWTHCONDITIONS
batch culture rep2, 10 min PGCGROWTHCONDITIONS
batch culture PGCGROWTHCONDITIONS
Cell were grown in 3-liter stirred tank bioreactor anaerobically. The growth medium contained Na2H2PO4 (1.1 g/l), K2HPO4 (2.5 g/l), (NH4)2SO4 (9.0 g/l), Glucose (15.0 g/l), CaCl2 (2.2 mg/l), MgSO4 (0.55 g/l), NaH2-Citrate (234 mg/l), FeCl3*6 H2O (25.0 mg/l), ZnSO4*7 H2O (0.18 mg/l), MnSO4*7 H2O (0.1 mg/l), CuSO4*5 H2O (0.16 mg/l), CoCl2*6 H2O (0.18 mg/l). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
gene counting: HTSeq-Count 0.6.0 PGCGROWTHCONDITIONS
Genome_build: NC007779.1 (UCSC Archaeal Genome Browser) PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were treated with RNAprotect (Qiagen, Hilden, Germany) and stored at -80°C until preparation. rRNA was removed using RiboZero rRNA Removal Kit (Illumina, San Diego, CA), and sequencing libraries were prepared with TruSeq™ RNA Sample Preparation Kitv2 (Illumina) PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The file format is .xlsx. The file contains the raw gene counts of all samples. PGCGROWTHCONDITIONS
time: 10 min PGCGROWTHCONDITIONS
Aeration was initiated at 1 l/min when the culture reached an OD (600nm) of 3. PGCGROWTHCONDITIONS
alignment: STAR 2.4.0i PGCGROWTHCONDITIONS
batch culture rep3, 0 min PGCGROWTHCONDITIONS
batch culture PGCGROWTHCONDITIONS
Cell were grown in 3-liter stirred tank bioreactor anaerobically. The growth medium contained Na2H2PO4 (1.1 g/l), K2HPO4 (2.5 g/l), (NH4)2SO4 (9.0 g/l), Glucose (15.0 g/l), CaCl2 (2.2 mg/l), MgSO4 (0.55 g/l), NaH2-Citrate (234 mg/l), FeCl3*6 H2O (25.0 mg/l), ZnSO4*7 H2O (0.18 mg/l), MnSO4*7 H2O (0.1 mg/l), CuSO4*5 H2O (0.16 mg/l), CoCl2*6 H2O (0.18 mg/l). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
gene counting: HTSeq-Count 0.6.0 PGCGROWTHCONDITIONS
Genome_build: NC007779.1 (UCSC Archaeal Genome Browser) PGCGROWTHCONDITIONS
replicate: 3 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were treated with RNAprotect (Qiagen, Hilden, Germany) and stored at -80°C until preparation. rRNA was removed using RiboZero rRNA Removal Kit (Illumina, San Diego, CA), and sequencing libraries were prepared with TruSeq™ RNA Sample Preparation Kitv2 (Illumina) PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The file format is .xlsx. The file contains the raw gene counts of all samples. PGCGROWTHCONDITIONS
time: 0 min PGCGROWTHCONDITIONS
Aeration was initiated at 1 l/min when the culture reached an OD (600nm) of 3. PGCGROWTHCONDITIONS
alignment: STAR 2.4.0i PGCGROWTHCONDITIONS
batch culture rep3, 0.5 min PGCGROWTHCONDITIONS
batch culture PGCGROWTHCONDITIONS
Cell were grown in 3-liter stirred tank bioreactor anaerobically. The growth medium contained Na2H2PO4 (1.1 g/l), K2HPO4 (2.5 g/l), (NH4)2SO4 (9.0 g/l), Glucose (15.0 g/l), CaCl2 (2.2 mg/l), MgSO4 (0.55 g/l), NaH2-Citrate (234 mg/l), FeCl3*6 H2O (25.0 mg/l), ZnSO4*7 H2O (0.18 mg/l), MnSO4*7 H2O (0.1 mg/l), CuSO4*5 H2O (0.16 mg/l), CoCl2*6 H2O (0.18 mg/l). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
gene counting: HTSeq-Count 0.6.0 PGCGROWTHCONDITIONS
Genome_build: NC007779.1 (UCSC Archaeal Genome Browser) PGCGROWTHCONDITIONS
replicate: 3 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were treated with RNAprotect (Qiagen, Hilden, Germany) and stored at -80°C until preparation. rRNA was removed using RiboZero rRNA Removal Kit (Illumina, San Diego, CA), and sequencing libraries were prepared with TruSeq™ RNA Sample Preparation Kitv2 (Illumina) PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The file format is .xlsx. The file contains the raw gene counts of all samples. PGCGROWTHCONDITIONS
time: 0.5 min PGCGROWTHCONDITIONS
Aeration was initiated at 1 l/min when the culture reached an OD (600nm) of 3. PGCGROWTHCONDITIONS
alignment: STAR 2.4.0i PGCGROWTHCONDITIONS
batch culture rep3, 1 min PGCGROWTHCONDITIONS
batch culture PGCGROWTHCONDITIONS
Cell were grown in 3-liter stirred tank bioreactor anaerobically. The growth medium contained Na2H2PO4 (1.1 g/l), K2HPO4 (2.5 g/l), (NH4)2SO4 (9.0 g/l), Glucose (15.0 g/l), CaCl2 (2.2 mg/l), MgSO4 (0.55 g/l), NaH2-Citrate (234 mg/l), FeCl3*6 H2O (25.0 mg/l), ZnSO4*7 H2O (0.18 mg/l), MnSO4*7 H2O (0.1 mg/l), CuSO4*5 H2O (0.16 mg/l), CoCl2*6 H2O (0.18 mg/l). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
gene counting: HTSeq-Count 0.6.0 PGCGROWTHCONDITIONS
Genome_build: NC007779.1 (UCSC Archaeal Genome Browser) PGCGROWTHCONDITIONS
replicate: 3 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were treated with RNAprotect (Qiagen, Hilden, Germany) and stored at -80°C until preparation. rRNA was removed using RiboZero rRNA Removal Kit (Illumina, San Diego, CA), and sequencing libraries were prepared with TruSeq™ RNA Sample Preparation Kitv2 (Illumina) PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The file format is .xlsx. The file contains the raw gene counts of all samples. PGCGROWTHCONDITIONS
time: 1 min PGCGROWTHCONDITIONS
Aeration was initiated at 1 l/min when the culture reached an OD (600nm) of 3. PGCGROWTHCONDITIONS
alignment: STAR 2.4.0i PGCGROWTHCONDITIONS
batch culture rep3, 2 min PGCGROWTHCONDITIONS
batch culture PGCGROWTHCONDITIONS
Cell were grown in 3-liter stirred tank bioreactor anaerobically. The growth medium contained Na2H2PO4 (1.1 g/l), K2HPO4 (2.5 g/l), (NH4)2SO4 (9.0 g/l), Glucose (15.0 g/l), CaCl2 (2.2 mg/l), MgSO4 (0.55 g/l), NaH2-Citrate (234 mg/l), FeCl3*6 H2O (25.0 mg/l), ZnSO4*7 H2O (0.18 mg/l), MnSO4*7 H2O (0.1 mg/l), CuSO4*5 H2O (0.16 mg/l), CoCl2*6 H2O (0.18 mg/l). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
gene counting: HTSeq-Count 0.6.0 PGCGROWTHCONDITIONS
Genome_build: NC007779.1 (UCSC Archaeal Genome Browser) PGCGROWTHCONDITIONS
replicate: 3 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were treated with RNAprotect (Qiagen, Hilden, Germany) and stored at -80°C until preparation. rRNA was removed using RiboZero rRNA Removal Kit (Illumina, San Diego, CA), and sequencing libraries were prepared with TruSeq™ RNA Sample Preparation Kitv2 (Illumina) PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The file format is .xlsx. The file contains the raw gene counts of all samples. PGCGROWTHCONDITIONS
time: 2 min PGCGROWTHCONDITIONS
Aeration was initiated at 1 l/min when the culture reached an OD (600nm) of 3. PGCGROWTHCONDITIONS
alignment: STAR 2.4.0i PGCGROWTHCONDITIONS
batch culture rep3, 5 min PGCGROWTHCONDITIONS
batch culture PGCGROWTHCONDITIONS
Cell were grown in 3-liter stirred tank bioreactor anaerobically. The growth medium contained Na2H2PO4 (1.1 g/l), K2HPO4 (2.5 g/l), (NH4)2SO4 (9.0 g/l), Glucose (15.0 g/l), CaCl2 (2.2 mg/l), MgSO4 (0.55 g/l), NaH2-Citrate (234 mg/l), FeCl3*6 H2O (25.0 mg/l), ZnSO4*7 H2O (0.18 mg/l), MnSO4*7 H2O (0.1 mg/l), CuSO4*5 H2O (0.16 mg/l), CoCl2*6 H2O (0.18 mg/l). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
gene counting: HTSeq-Count 0.6.0 PGCGROWTHCONDITIONS
Genome_build: NC007779.1 (UCSC Archaeal Genome Browser) PGCGROWTHCONDITIONS
replicate: 3 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were treated with RNAprotect (Qiagen, Hilden, Germany) and stored at -80°C until preparation. rRNA was removed using RiboZero rRNA Removal Kit (Illumina, San Diego, CA), and sequencing libraries were prepared with TruSeq™ RNA Sample Preparation Kitv2 (Illumina) PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The file format is .xlsx. The file contains the raw gene counts of all samples. PGCGROWTHCONDITIONS
time: 5 min PGCGROWTHCONDITIONS
Aeration was initiated at 1 l/min when the culture reached an OD (600nm) of 3. PGCGROWTHCONDITIONS
alignment: STAR 2.4.0i PGCGROWTHCONDITIONS
batch culture rep3, 10 min PGCGROWTHCONDITIONS
batch culture PGCGROWTHCONDITIONS
Cell were grown in 3-liter stirred tank bioreactor anaerobically. The growth medium contained Na2H2PO4 (1.1 g/l), K2HPO4 (2.5 g/l), (NH4)2SO4 (9.0 g/l), Glucose (15.0 g/l), CaCl2 (2.2 mg/l), MgSO4 (0.55 g/l), NaH2-Citrate (234 mg/l), FeCl3*6 H2O (25.0 mg/l), ZnSO4*7 H2O (0.18 mg/l), MnSO4*7 H2O (0.1 mg/l), CuSO4*5 H2O (0.16 mg/l), CoCl2*6 H2O (0.18 mg/l). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
gene counting: HTSeq-Count 0.6.0 PGCGROWTHCONDITIONS
Genome_build: NC007779.1 (UCSC Archaeal Genome Browser) PGCGROWTHCONDITIONS
replicate: 3 PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were treated with RNAprotect (Qiagen, Hilden, Germany) and stored at -80°C until preparation. rRNA was removed using RiboZero rRNA Removal Kit (Illumina, San Diego, CA), and sequencing libraries were prepared with TruSeq™ RNA Sample Preparation Kitv2 (Illumina) PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The file format is .xlsx. The file contains the raw gene counts of all samples. PGCGROWTHCONDITIONS
time: 10 min PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: WT PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
Parent LB rep1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, WT, LB and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: WT PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
Parent LB rep2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, WT, LB and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
cysG KO LB rep1 PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: cysG knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, cysG KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
cysG KO LB rep2 PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: cysG knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, cysG KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
cysH KO LB rep1 PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: cysH knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, cysH KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
cysH KO LB rep2 PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: cysH knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, cysH KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
dcd KO LB rep1 PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: dcd knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, dcd KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
dcd KO LB rep2 PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: dcd knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, dcd KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
fadr KO LB rep1 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: fadR knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, fadR KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
fadr KO LB rep2 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: fadR knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, fadR KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: ppk knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
ppk KO LB rep1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, ppk KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: ppk knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
ppk KO LB rep2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, ppk KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: wzc knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, wzc KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
wzc KO LB rep1 PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: wzc knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, wzc KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
wzc KO LB rep2 PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: yghD knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, yghD KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
yghD KO LB rep1 PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: yghD knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, yghD KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
yghD KO LB rep2 PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
fepA KO LB rep1 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: fepA knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, fepA KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
fepA KO LB rep2 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: fepA knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, fepA KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: lacA knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
lacA KO LB rep1 PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, lacA KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: lacA knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
lacA KO LB rep2 PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: LB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, lacA KO, LB and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: WT PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
Parent M9 rep1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, WT, M9 and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: WT PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
Parent M9 rep2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, WT, M9 and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
dcd KO M9 rep1 PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: dcd knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, dcd KO, M9 and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
dcd KO M9 rep2 PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: dcd knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, dcd KO, M9 and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
fadr KO M9 rep2 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: fadR knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, fadR KO, M9 and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: ppk knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
ppk KO M9 rep1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, ppk KO, M9 and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: ppk knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
ppk KO M9 rep2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, ppk KO, M9 and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: wzc knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, wzc KO, M9 and 0.3% glucose PGCGROWTHCONDITIONS
wzc KO M9 rep1 PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: wzc knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, wzc KO, M9 and 0.3% glucose PGCGROWTHCONDITIONS
wzc KO M9 rep2 PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: yghD knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, yghD KO, M9 and 0.3% glucose PGCGROWTHCONDITIONS
yghD KO M9 rep1 PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: yghD knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, yghD KO, M9 and 0.3% glucose PGCGROWTHCONDITIONS
yghD KO M9 rep2 PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
fepA KO M9 rep1 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: fepA knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, fepA KO, M9 and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
fepA KO M9 rep2 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: fepA knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, fepA KO, M9 and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: lacA knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
lacA KO M9 rep1 PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, lacA KO, M9 and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: lacA knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
lacA KO M9 rep2 PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.3% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, lacA KO, M9 and 0.3% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: WT PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, WT, M9 and 0.4% glucose PGCGROWTHCONDITIONS
WT rep1 PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: WT PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, WT, M9 and 0.4% glucose PGCGROWTHCONDITIONS
WT rep2 PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: WT PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, WT, M9 and 0.4% glucose PGCGROWTHCONDITIONS
WT rep3 PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: mgtA knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
mgtA KO rep1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, mgtA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: mgtA knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
mgtA KO rep2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, mgtA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: mgtA knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
mgtA KO rep3 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, mgtA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
gabT KO rep1 PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: gabT knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, gabT KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
gabT KO rep2 PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: gabT knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, gabT KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
gabT KO rep3 PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: gabT knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, gabT KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: sdhC knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sdhC KO rep1 PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, sdhC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: sdhC knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sdhC KO rep2 PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, sdhC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: sdhC knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sdhC KO rep3 PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, sdhC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: putP knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
putP KO rep1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, putP KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: putP knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
putP KO rep2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, putP KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: putP knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
putP KO rep3 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, putP KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: rfbA knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
rfbA KO rep1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, rfbA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: rfbA knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
rfbA KO rep3 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, rfbA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
entF KO rep1 PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: entF knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, entF KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
entF KO rep2 PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: entF knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, entF KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
entF KO rep3 PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: entF knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, entF KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: kefB knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
kefB KO rep1 PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, kefB KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: kefB knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
kefB KO rep2 PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, kefB KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: kefB knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
kefB KO rep3 PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, kefB KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
cysA KO rep1 PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: cysA knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, cysA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
cysA KO rep2 PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: cysA knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, cysA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
cysA KO rep3 PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: cysA knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, cysA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
galE KO rep1 PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: galE knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, galE KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
galE KO rep2 PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: galE knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, galE KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
galE KO rep3 PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: galE knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, galE KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: mhpD knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
mhpD KO rep1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, mhpD KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: mhpD knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
mhpD KO rep2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, mhpD KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: mhpD knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
mhpD KO rep3 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, mhpD KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
fliY KO rep1 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: fliY knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, fliY KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
fliY KO rep2 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: fliY knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, fliY KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
fliY KO rep3 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: fliY knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, fliY KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: lplA knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
lplA KO rep1 PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, lplA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: lplA knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
lplA KO rep2 PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, lplA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: lplA knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
lplA KO rep3 PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, lplA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: khc knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
khc KO rep1 PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, khc KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: khc knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
khc KO rep2 PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, khc KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: khc knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
khc KO rep3 PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, khc KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: ugpC knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
ugpC KO rep1 PGCGROWTHCONDITIONS
Whole cell, ugpC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: ugpC knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
ugpC KO rep2 PGCGROWTHCONDITIONS
Whole cell, ugpC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: ugpC knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
ugpC KO rep3 PGCGROWTHCONDITIONS
Whole cell, ugpC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: trpD knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
trpD KO rep1 PGCGROWTHCONDITIONS
Whole cell, trpD KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: trpD knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
trpD KO rep2 PGCGROWTHCONDITIONS
Whole cell, trpD KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: trpD knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
trpD KO rep3 PGCGROWTHCONDITIONS
Whole cell, trpD KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
aspC KO rep1 PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: aspC knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, aspC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
aspC KO rep2 PGCGROWTHCONDITIONS
Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
Escherichia coli BW25113 PGCGROWTHCONDITIONS
For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: aspC knockout PGCGROWTHCONDITIONS
HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
media: M9 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain/background: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
treatment: 0.4% glucose PGCGROWTHCONDITIONS
Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
Whole cell, aspC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS
All raw FastQ files generated were filtered using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). PGCGROWTHCONDITIONS
Enterohemorrhagic Escherichia coli O157:H7 strain EDL933 PGCGROWTHCONDITIONS
Escherichia coli O157:H7 str. EDL933 PGCGROWTHCONDITIONS
Genome_build: NC_002655.2 PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
Illumina Casava1.7 software used for basecalling. PGCGROWTHCONDITIONS
Overnight cultures of bacteria were diluted 1:100 in fresh LB broth and grown to logarithmic phase at an OD600 of about 0.8. PGCGROWTHCONDITIONS
phase: logarithmic phase PGCGROWTHCONDITIONS
Reads per kilobase of exon model per million mapped reads (RPKM) was used as a normalized metric to present the gene expression levels.(Nature methods 2008, 5: 621-628) PGCGROWTHCONDITIONS
RNA extraction was performed using RiboPure-BacteriaTM Bacteria kit according to the manufacturer's protocol (Ambion, Life Technologies). DNase I treatment was applied to eliminate genomic DNA contamination as per the manufacturer's recommendations. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPKM PGCGROWTHCONDITIONS
The bacteria were centrifuged at 4000×g at 4°C for 5 min and then washed with PBS. PGCGROWTHCONDITIONS
Transcripts evaluation of differential expression were accomplished using MARS (MA-plot-based method with Random sampling model) in DEGseq package.(Bioinformatics 2010, 26: 136-138) PGCGROWTHCONDITIONS
wt_1 PGCGROWTHCONDITIONS
All raw FastQ files generated were filtered using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). PGCGROWTHCONDITIONS
Enterohemorrhagic Escherichia coli O157:H7 strain EDL933 PGCGROWTHCONDITIONS
Escherichia coli O157:H7 str. EDL933 PGCGROWTHCONDITIONS
Genome_build: NC_002655.2 PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
Illumina Casava1.7 software used for basecalling. PGCGROWTHCONDITIONS
Overnight cultures of bacteria were diluted 1:100 in fresh LB broth and grown to logarithmic phase at an OD600 of about 0.8. PGCGROWTHCONDITIONS
phase: logarithmic phase PGCGROWTHCONDITIONS
Reads per kilobase of exon model per million mapped reads (RPKM) was used as a normalized metric to present the gene expression levels.(Nature methods 2008, 5: 621-628) PGCGROWTHCONDITIONS
RNA extraction was performed using RiboPure-BacteriaTM Bacteria kit according to the manufacturer's protocol (Ambion, Life Technologies). DNase I treatment was applied to eliminate genomic DNA contamination as per the manufacturer's recommendations. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPKM PGCGROWTHCONDITIONS
The bacteria were centrifuged at 4000×g at 4°C for 5 min and then washed with PBS. PGCGROWTHCONDITIONS
Transcripts evaluation of differential expression were accomplished using MARS (MA-plot-based method with Random sampling model) in DEGseq package.(Bioinformatics 2010, 26: 136-138) PGCGROWTHCONDITIONS
wt_2 PGCGROWTHCONDITIONS
All raw FastQ files generated were filtered using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). PGCGROWTHCONDITIONS
Enterohemorrhagic Escherichia coli O157:H7 strain EDL933 PGCGROWTHCONDITIONS
Escherichia coli O157:H7 str. EDL933 PGCGROWTHCONDITIONS
Genome_build: NC_002655.2 PGCGROWTHCONDITIONS
genotype: {delta}hns PGCGROWTHCONDITIONS
hns_1 PGCGROWTHCONDITIONS
Illumina Casava1.7 software used for basecalling. PGCGROWTHCONDITIONS
Overnight cultures of bacteria were diluted 1:100 in fresh LB broth and grown to logarithmic phase at an OD600 of about 0.8. PGCGROWTHCONDITIONS
phase: logarithmic phase PGCGROWTHCONDITIONS
Reads per kilobase of exon model per million mapped reads (RPKM) was used as a normalized metric to present the gene expression levels.(Nature methods 2008, 5: 621-628) PGCGROWTHCONDITIONS
RNA extraction was performed using RiboPure-BacteriaTM Bacteria kit according to the manufacturer's protocol (Ambion, Life Technologies). DNase I treatment was applied to eliminate genomic DNA contamination as per the manufacturer's recommendations. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPKM PGCGROWTHCONDITIONS
The bacteria were centrifuged at 4000×g at 4°C for 5 min and then washed with PBS. PGCGROWTHCONDITIONS
Transcripts evaluation of differential expression were accomplished using MARS (MA-plot-based method with Random sampling model) in DEGseq package.(Bioinformatics 2010, 26: 136-138) PGCGROWTHCONDITIONS
All raw FastQ files generated were filtered using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). PGCGROWTHCONDITIONS
Enterohemorrhagic Escherichia coli O157:H7 strain EDL933 PGCGROWTHCONDITIONS
Escherichia coli O157:H7 str. EDL933 PGCGROWTHCONDITIONS
Genome_build: NC_002655.2 PGCGROWTHCONDITIONS
genotype: {delta}hns PGCGROWTHCONDITIONS
hns_2 PGCGROWTHCONDITIONS
Illumina Casava1.7 software used for basecalling. PGCGROWTHCONDITIONS
Overnight cultures of bacteria were diluted 1:100 in fresh LB broth and grown to logarithmic phase at an OD600 of about 0.8. PGCGROWTHCONDITIONS
phase: logarithmic phase PGCGROWTHCONDITIONS
Reads per kilobase of exon model per million mapped reads (RPKM) was used as a normalized metric to present the gene expression levels.(Nature methods 2008, 5: 621-628) PGCGROWTHCONDITIONS
RNA extraction was performed using RiboPure-BacteriaTM Bacteria kit according to the manufacturer's protocol (Ambion, Life Technologies). DNase I treatment was applied to eliminate genomic DNA contamination as per the manufacturer's recommendations. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPKM PGCGROWTHCONDITIONS
The bacteria were centrifuged at 4000×g at 4°C for 5 min and then washed with PBS. PGCGROWTHCONDITIONS
Transcripts evaluation of differential expression were accomplished using MARS (MA-plot-based method with Random sampling model) in DEGseq package.(Bioinformatics 2010, 26: 136-138) PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: Wild-type PGCGROWTHCONDITIONS
growth phase: Early Exponential PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
wt_EE_1 PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: Wild-type PGCGROWTHCONDITIONS
growth phase: Early Exponential PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
wt_EE_2 PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rsd PGCGROWTHCONDITIONS
growth phase: Early Exponential PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rsd_EE_1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rsd PGCGROWTHCONDITIONS
growth phase: Early Exponential PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rsd_EE_2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del ssrS PGCGROWTHCONDITIONS
growth phase: Early Exponential PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
ssrS_EE_1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del ssrS PGCGROWTHCONDITIONS
growth phase: Early Exponential PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
ssrS_EE_2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rsd; del ssrS PGCGROWTHCONDITIONS
growth phase: Early Exponential PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rsdssrS_EE_1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rsd; del ssrS PGCGROWTHCONDITIONS
growth phase: Early Exponential PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rsdssrS_EE_2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rpoS PGCGROWTHCONDITIONS
growth phase: Early Exponential PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rpoS_EE_1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rpoS PGCGROWTHCONDITIONS
growth phase: Early Exponential PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rpoS_EE_2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: Wild-type PGCGROWTHCONDITIONS
growth phase: Mid-Exponential PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
wt_ME_1 PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: Wild-type PGCGROWTHCONDITIONS
growth phase: Mid-Exponential PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
wt_ME_2 PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rsd PGCGROWTHCONDITIONS
growth phase: Mid-Exponential PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rsd_ME_1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rsd PGCGROWTHCONDITIONS
growth phase: Mid-Exponential PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rsd_ME_2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del ssrS PGCGROWTHCONDITIONS
growth phase: Mid-Exponential PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
ssrS_ME_1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del ssrS PGCGROWTHCONDITIONS
growth phase: Mid-Exponential PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
ssrS_ME_2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rsd; del ssrS PGCGROWTHCONDITIONS
growth phase: Mid-Exponential PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rsdssrS_ME_1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rsd; del ssrS PGCGROWTHCONDITIONS
growth phase: Mid-Exponential PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rsdssrS_ME_2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rpoS PGCGROWTHCONDITIONS
growth phase: Mid-Exponential PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rpoS_ME_1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rpoS PGCGROWTHCONDITIONS
growth phase: Mid-Exponential PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rpoS_ME_2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: Wild-type PGCGROWTHCONDITIONS
growth phase: Transition to Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
wt_TS_1 PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: Wild-type PGCGROWTHCONDITIONS
growth phase: Transition to Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
wt_TS_2 PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rsd PGCGROWTHCONDITIONS
growth phase: Transition to Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rsd_TS_1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rsd PGCGROWTHCONDITIONS
growth phase: Transition to Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rsd_TS_2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del ssrS PGCGROWTHCONDITIONS
growth phase: Transition to Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
ssrS_TS_1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del ssrS PGCGROWTHCONDITIONS
growth phase: Transition to Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
ssrS_TS_2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rsd; del ssrS PGCGROWTHCONDITIONS
growth phase: Transition to Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rsdssrS_TS_1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rsd; del ssrS PGCGROWTHCONDITIONS
growth phase: Transition to Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rsdssrS_TS_2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rpoS PGCGROWTHCONDITIONS
growth phase: Transition to Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rpoS_TS_1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rpoS PGCGROWTHCONDITIONS
growth phase: Transition to Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rpoS_TS_2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: Wild-type PGCGROWTHCONDITIONS
growth phase: Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
wt_S_1 PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: Wild-type PGCGROWTHCONDITIONS
growth phase: Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
wt_S_2 PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rsd PGCGROWTHCONDITIONS
growth phase: Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rsd_S_1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rsd PGCGROWTHCONDITIONS
growth phase: Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rsd_S_2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del ssrS PGCGROWTHCONDITIONS
growth phase: Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
ssrS_S_1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del ssrS PGCGROWTHCONDITIONS
growth phase: Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
ssrS_S_2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rsd; del ssrS PGCGROWTHCONDITIONS
growth phase: Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rsdssrS_S_1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rsd; del ssrS PGCGROWTHCONDITIONS
growth phase: Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rsdssrS_S_2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rpoS PGCGROWTHCONDITIONS
growth phase: Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rpoS_S_1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rpoS PGCGROWTHCONDITIONS
growth phase: Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rpoS_S_2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: Wild-type PGCGROWTHCONDITIONS
growth phase: Late Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
wt_LS_2 PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rsd PGCGROWTHCONDITIONS
growth phase: Late Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rsd_LS_1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rsd PGCGROWTHCONDITIONS
growth phase: Late Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rsd_LS_2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del ssrS PGCGROWTHCONDITIONS
growth phase: Late Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
ssrS_LS_1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del ssrS PGCGROWTHCONDITIONS
growth phase: Late Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
ssrS_LS_2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rsd; del ssrS PGCGROWTHCONDITIONS
growth phase: Late Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rsdssrS_LS_1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rsd; del ssrS PGCGROWTHCONDITIONS
growth phase: Late Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rsdssrS_LS_2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rpoS PGCGROWTHCONDITIONS
growth phase: Late Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rpoS_LS_1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Bacterial cells PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype: del rpoS PGCGROWTHCONDITIONS
growth phase: Late Stationary PGCGROWTHCONDITIONS
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer. PGCGROWTHCONDITIONS
M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS
Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth. PGCGROWTHCONDITIONS
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water. PGCGROWTHCONDITIONS
rpoS_LS_2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample. PGCGROWTHCONDITIONS
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype. PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WT PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 0 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTRep1_0min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WT PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 2 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTRep1_2min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WT PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 4 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTRep1_4min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WT PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 6 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTRep1_6min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WT PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 8 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTRep1_8min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WT PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 10 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTRep1_10min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WT PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 15 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTRep1_15min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WT PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 20 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTRep1_20min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WT PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 0 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTRep2_0min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WT PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 2 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTRep2_2min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WT PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 4 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTRep2_4min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WT PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 6 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTRep2_6min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WT PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 8 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTRep2_8min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WT PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 10 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTRep2_10min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WT PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 15 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTRep2_15min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WT PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 20 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTRep2_20min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WTKas PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 0 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTKasRep1_0min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WTKas PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 2 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTKasRep1_2min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WTKas PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 4 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTKasRep1_4min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WTKas PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 6 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTKasRep1_6min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WTKas PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 8 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTKasRep1_8min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WTKas PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 15 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTKasRep1_15min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WTKas PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 20 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTKasRep1_20min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WTKas PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 0 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTKasRep2_0min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WTKas PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 2 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTKasRep2_2min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WTKas PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 4 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTKasRep2_4min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WTKas PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 6 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTKasRep2_6min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WTKas PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 8 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTKasRep2_8min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WTKas PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 10 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTKasRep2_10min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WTKas PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 15 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTKasRep2_15min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: WTKas PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 20 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
WTKasRep2_20min PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: Mut PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
MutRep1_0min PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 0 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: Mut PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
MutRep1_2min PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 2 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: Mut PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
MutRep1_4min PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 4 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: Mut PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
MutRep1_6min PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 6 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: Mut PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
MutRep1_8min PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 8 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: Mut PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
MutRep1_10min PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 10 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: Mut PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
MutRep1_15min PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 15 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: Mut PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
MutRep1_20min PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 20 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: Mut PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
MutRep2_0min PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 0 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: Mut PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
MutRep2_2min PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 2 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: Mut PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
MutRep2_4min PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 4 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: Mut PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
MutRep2_6min PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 6 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: Mut PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
MutRep2_8min PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 8 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: Mut PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
MutRep2_10min PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 10 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: Mut PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
MutRep2_15min PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 15 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: Mut PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
MutRep2_20min PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 20 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol. PGCGROWTHCONDITIONS
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox PGCGROWTHCONDITIONS
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2. PGCGROWTHCONDITIONS
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
genotype/variaion: mMaple3 PGCGROWTHCONDITIONS
mg1655 PGCGROWTHCONDITIONS
mMaple3_2min PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: sam containing aligned sequences PGCGROWTHCONDITIONS
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization. PGCGROWTHCONDITIONS
time point: 2 min PGCGROWTHCONDITIONS
treatment: rifampicin PGCGROWTHCONDITIONS
Basecalls performed using HCS 2.0.5 and RTA 1.17.20 PGCGROWTHCONDITIONS
Escherichia coli_control condition PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression (based on known genes) was determined using Cufflinks 2.0.2, only PF reads were retained PGCGROWTHCONDITIONS
Genome_build: W3110  (NC_007779) PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
growth phase: log phase PGCGROWTHCONDITIONS
Library preparation were performed with Epicentre ScriptseqTM v2 RNA-Seq Library preparation kit with 50 ng of depleted RNA; Strand orientated RNA-Seq PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-seq reads were aligned to the W3110 genome  using CASAVA 1.8.2 PGCGROWTHCONDITIONS
Rodrigue_1-WT-phiNi-1 PGCGROWTHCONDITIONS
strain: W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file with coverage and FPKM measurements PGCGROWTHCONDITIONS
Total RNA was extracted using the frozen acid-phenol method described by Maes and Messens (Maes and Messens, 1992) and then treated with RNase-free DNaseI according to the manufacturer’s recommendations (Ambion, USA). PGCGROWTHCONDITIONS
Transcriptomic analyses were carried out after growing bacteria in minimal media supplemented with glucose. Several Ni concentrations and exposure times were assayed. rcnA gene expression was taken as an internal control to arbitrate between the different conditions. rcnA is induced by Ni when cells are overloaded with this ion and must detoxify the cytoplasm by extruding excess metal via the RcnAB efflux system. rcnA induction was maximised after culture incubation for 10 min, and longer periods of incubation lead to a decline in rcnA expression (Fig. S1). For the RNA-Seq experiments, bacteria were grown until O.D600nm = 0.3, were treated with 50 µM NiCl2 for 10 min and were frozen prior to RNA extraction. PGCGROWTHCONDITIONS
Basecalls performed using HCS 2.0.5 and RTA 1.17.20 PGCGROWTHCONDITIONS
Escherichia coli_control condition PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression (based on known genes) was determined using Cufflinks 2.0.2, only PF reads were retained PGCGROWTHCONDITIONS
Genome_build: W3110  (NC_007779) PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
growth phase: log phase PGCGROWTHCONDITIONS
Library preparation were performed with Epicentre ScriptseqTM v2 RNA-Seq Library preparation kit with 50 ng of depleted RNA; Strand orientated RNA-Seq PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-seq reads were aligned to the W3110 genome  using CASAVA 1.8.2 PGCGROWTHCONDITIONS
Rodrigue_6-WT-phiNi-2 PGCGROWTHCONDITIONS
strain: W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file with coverage and FPKM measurements PGCGROWTHCONDITIONS
Total RNA was extracted using the frozen acid-phenol method described by Maes and Messens (Maes and Messens, 1992) and then treated with RNase-free DNaseI according to the manufacturer’s recommendations (Ambion, USA). PGCGROWTHCONDITIONS
Transcriptomic analyses were carried out after growing bacteria in minimal media supplemented with glucose. Several Ni concentrations and exposure times were assayed. rcnA gene expression was taken as an internal control to arbitrate between the different conditions. rcnA is induced by Ni when cells are overloaded with this ion and must detoxify the cytoplasm by extruding excess metal via the RcnAB efflux system. rcnA induction was maximised after culture incubation for 10 min, and longer periods of incubation lead to a decline in rcnA expression (Fig. S1). For the RNA-Seq experiments, bacteria were grown until O.D600nm = 0.3, were treated with 50 µM NiCl2 for 10 min and were frozen prior to RNA extraction. PGCGROWTHCONDITIONS
Basecalls performed using HCS 2.0.5 and RTA 1.17.20 PGCGROWTHCONDITIONS
Escherichia coli_control condition PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression (based on known genes) was determined using Cufflinks 2.0.2, only PF reads were retained PGCGROWTHCONDITIONS
Genome_build: W3110  (NC_007779) PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
growth phase: log phase PGCGROWTHCONDITIONS
Library preparation were performed with Epicentre ScriptseqTM v2 RNA-Seq Library preparation kit with 50 ng of depleted RNA; Strand orientated RNA-Seq PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-seq reads were aligned to the W3110 genome  using CASAVA 1.8.2 PGCGROWTHCONDITIONS
Rodrigue_9-WT-phiNi-3 PGCGROWTHCONDITIONS
strain: W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file with coverage and FPKM measurements PGCGROWTHCONDITIONS
Total RNA was extracted using the frozen acid-phenol method described by Maes and Messens (Maes and Messens, 1992) and then treated with RNase-free DNaseI according to the manufacturer’s recommendations (Ambion, USA). PGCGROWTHCONDITIONS
Transcriptomic analyses were carried out after growing bacteria in minimal media supplemented with glucose. Several Ni concentrations and exposure times were assayed. rcnA gene expression was taken as an internal control to arbitrate between the different conditions. rcnA is induced by Ni when cells are overloaded with this ion and must detoxify the cytoplasm by extruding excess metal via the RcnAB efflux system. rcnA induction was maximised after culture incubation for 10 min, and longer periods of incubation lead to a decline in rcnA expression (Fig. S1). For the RNA-Seq experiments, bacteria were grown until O.D600nm = 0.3, were treated with 50 µM NiCl2 for 10 min and were frozen prior to RNA extraction. PGCGROWTHCONDITIONS
Basecalls performed using HCS 2.0.5 and RTA 1.17.20 PGCGROWTHCONDITIONS
Escherichia coli_nickel condition PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression (based on known genes) was determined using Cufflinks 2.0.2, only PF reads were retained PGCGROWTHCONDITIONS
Genome_build: W3110  (NC_007779) PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
growth phase: log phase PGCGROWTHCONDITIONS
Library preparation were performed with Epicentre ScriptseqTM v2 RNA-Seq Library preparation kit with 50 ng of depleted RNA; Strand orientated RNA-Seq PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-seq reads were aligned to the W3110 genome  using CASAVA 1.8.2 PGCGROWTHCONDITIONS
Rodrigue_2-WT-Ni-1 PGCGROWTHCONDITIONS
strain: W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file with coverage and FPKM measurements PGCGROWTHCONDITIONS
Total RNA was extracted using the frozen acid-phenol method described by Maes and Messens (Maes and Messens, 1992) and then treated with RNase-free DNaseI according to the manufacturer’s recommendations (Ambion, USA). PGCGROWTHCONDITIONS
Transcriptomic analyses were carried out after growing bacteria in minimal media supplemented with glucose. Several Ni concentrations and exposure times were assayed. rcnA gene expression was taken as an internal control to arbitrate between the different conditions. rcnA is induced by Ni when cells are overloaded with this ion and must detoxify the cytoplasm by extruding excess metal via the RcnAB efflux system. rcnA induction was maximised after culture incubation for 10 min, and longer periods of incubation lead to a decline in rcnA expression (Fig. S1). For the RNA-Seq experiments, bacteria were grown until O.D600nm = 0.3, were treated with 50 µM NiCl2 for 10 min and were frozen prior to RNA extraction. PGCGROWTHCONDITIONS
Basecalls performed using HCS 2.0.5 and RTA 1.17.20 PGCGROWTHCONDITIONS
Escherichia coli_nickel condition PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression (based on known genes) was determined using Cufflinks 2.0.2, only PF reads were retained PGCGROWTHCONDITIONS
Genome_build: W3110  (NC_007779) PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
growth phase: log phase PGCGROWTHCONDITIONS
Library preparation were performed with Epicentre ScriptseqTM v2 RNA-Seq Library preparation kit with 50 ng of depleted RNA; Strand orientated RNA-Seq PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-seq reads were aligned to the W3110 genome  using CASAVA 1.8.2 PGCGROWTHCONDITIONS
Rodrigue_5-WT-Ni-2 PGCGROWTHCONDITIONS
strain: W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file with coverage and FPKM measurements PGCGROWTHCONDITIONS
Total RNA was extracted using the frozen acid-phenol method described by Maes and Messens (Maes and Messens, 1992) and then treated with RNase-free DNaseI according to the manufacturer’s recommendations (Ambion, USA). PGCGROWTHCONDITIONS
Transcriptomic analyses were carried out after growing bacteria in minimal media supplemented with glucose. Several Ni concentrations and exposure times were assayed. rcnA gene expression was taken as an internal control to arbitrate between the different conditions. rcnA is induced by Ni when cells are overloaded with this ion and must detoxify the cytoplasm by extruding excess metal via the RcnAB efflux system. rcnA induction was maximised after culture incubation for 10 min, and longer periods of incubation lead to a decline in rcnA expression (Fig. S1). For the RNA-Seq experiments, bacteria were grown until O.D600nm = 0.3, were treated with 50 µM NiCl2 for 10 min and were frozen prior to RNA extraction. PGCGROWTHCONDITIONS
Basecalls performed using HCS 2.0.5 and RTA 1.17.20 PGCGROWTHCONDITIONS
Escherichia coli_nickel condition PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gene expression (based on known genes) was determined using Cufflinks 2.0.2, only PF reads were retained PGCGROWTHCONDITIONS
Genome_build: W3110  (NC_007779) PGCGROWTHCONDITIONS
genotype: wild type PGCGROWTHCONDITIONS
growth phase: log phase PGCGROWTHCONDITIONS
Library preparation were performed with Epicentre ScriptseqTM v2 RNA-Seq Library preparation kit with 50 ng of depleted RNA; Strand orientated RNA-Seq PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-seq reads were aligned to the W3110 genome  using CASAVA 1.8.2 PGCGROWTHCONDITIONS
Rodrigue_10-WT-Ni-3 PGCGROWTHCONDITIONS
strain: W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file with coverage and FPKM measurements PGCGROWTHCONDITIONS
Total RNA was extracted using the frozen acid-phenol method described by Maes and Messens (Maes and Messens, 1992) and then treated with RNase-free DNaseI according to the manufacturer’s recommendations (Ambion, USA). PGCGROWTHCONDITIONS
Transcriptomic analyses were carried out after growing bacteria in minimal media supplemented with glucose. Several Ni concentrations and exposure times were assayed. rcnA gene expression was taken as an internal control to arbitrate between the different conditions. rcnA is induced by Ni when cells are overloaded with this ion and must detoxify the cytoplasm by extruding excess metal via the RcnAB efflux system. rcnA induction was maximised after culture incubation for 10 min, and longer periods of incubation lead to a decline in rcnA expression (Fig. S1). For the RNA-Seq experiments, bacteria were grown until O.D600nm = 0.3, were treated with 50 µM NiCl2 for 10 min and were frozen prior to RNA extraction. PGCGROWTHCONDITIONS
E. coli cells were grown in Luria Broth supplemented with 100ug/ml ampicillin to retain the plasmids. PGCGROWTHCONDITIONS
E. coli cells were grown until mid-exponential phase and treated with 0.5mM isopropyl-β-d-thiogalactopyranoside (IPTG) to induce expression of the empty vector or the small RNA. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 subst. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: delta dicF, lacIq PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba, Adhya and Crombrugge. J. Bio Chem. 1981, 256: p11905-11910 PGCGROWTHCONDITIONS
protocol: vector control PGCGROWTHCONDITIONS
Ribosomal RNA was removed from 1 μg of total RNA using Ribozero rRNA Removal Meta-Bacteria Kit (Epicentre Biotechnologies) and the mRNA-enriched fraction was converted to indexed RNA-seq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel formatted matrix table containing transcript coordinates, normalized abundance estimates across the biological replicates and fold-changes in gene expression between cells expressing Vector and DicF. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed-VectorvsDicF-operon.txt: .txt tab delimited file with operons expressed differently between vector and DicF PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed-VectorvsDicF-transcripts.txt: .txt raw output file from Rockhopper PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed-VectorvsDicF-transcripts.xlsx: Excel file with transcription start and stop, expression values of all genes in the E. coli genome in vector and DicF PGCGROWTHCONDITIONS
The program Rockhopper (described in Mc Clure, et al. Nucleic Acids Research. 2013, 41(14)) was used for alignment, normalization, and quantification. Genome_builg: K-12 subst. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Vector rep1 PGCGROWTHCONDITIONS
E. coli cells were grown in Luria Broth supplemented with 100ug/ml ampicillin to retain the plasmids. PGCGROWTHCONDITIONS
E. coli cells were grown until mid-exponential phase and treated with 0.5mM isopropyl-β-d-thiogalactopyranoside (IPTG) to induce expression of the empty vector or the small RNA. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 subst. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: delta dicF, lacIq PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba, Adhya and Crombrugge. J. Bio Chem. 1981, 256: p11905-11910 PGCGROWTHCONDITIONS
protocol: vector control PGCGROWTHCONDITIONS
Ribosomal RNA was removed from 1 μg of total RNA using Ribozero rRNA Removal Meta-Bacteria Kit (Epicentre Biotechnologies) and the mRNA-enriched fraction was converted to indexed RNA-seq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel formatted matrix table containing transcript coordinates, normalized abundance estimates across the biological replicates and fold-changes in gene expression between cells expressing Vector and DicF. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed-VectorvsDicF-operon.txt: .txt tab delimited file with operons expressed differently between vector and DicF PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed-VectorvsDicF-transcripts.txt: .txt raw output file from Rockhopper PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed-VectorvsDicF-transcripts.xlsx: Excel file with transcription start and stop, expression values of all genes in the E. coli genome in vector and DicF PGCGROWTHCONDITIONS
The program Rockhopper (described in Mc Clure, et al. Nucleic Acids Research. 2013, 41(14)) was used for alignment, normalization, and quantification. Genome_builg: K-12 subst. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Vector rep2 PGCGROWTHCONDITIONS
E. coli cells were grown in Luria Broth supplemented with 100ug/ml ampicillin to retain the plasmids. PGCGROWTHCONDITIONS
E. coli cells were grown until mid-exponential phase and treated with 0.5mM isopropyl-β-d-thiogalactopyranoside (IPTG) to induce expression of the empty vector or the small RNA. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 subst. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: delta dicF, lacIq PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba, Adhya and Crombrugge. J. Bio Chem. 1981, 256: p11905-11910 PGCGROWTHCONDITIONS
protocol: vector control PGCGROWTHCONDITIONS
Ribosomal RNA was removed from 1 μg of total RNA using Ribozero rRNA Removal Meta-Bacteria Kit (Epicentre Biotechnologies) and the mRNA-enriched fraction was converted to indexed RNA-seq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel formatted matrix table containing transcript coordinates, normalized abundance estimates across the biological replicates and fold-changes in gene expression between cells expressing Vector and DicF. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed-VectorvsDicF-operon.txt: .txt tab delimited file with operons expressed differently between vector and DicF PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed-VectorvsDicF-transcripts.txt: .txt raw output file from Rockhopper PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed-VectorvsDicF-transcripts.xlsx: Excel file with transcription start and stop, expression values of all genes in the E. coli genome in vector and DicF PGCGROWTHCONDITIONS
The program Rockhopper (described in Mc Clure, et al. Nucleic Acids Research. 2013, 41(14)) was used for alignment, normalization, and quantification. Genome_builg: K-12 subst. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
Vector rep3 PGCGROWTHCONDITIONS
DicF rep1 PGCGROWTHCONDITIONS
E. coli cells were grown in Luria Broth supplemented with 100ug/ml ampicillin to retain the plasmids. PGCGROWTHCONDITIONS
E. coli cells were grown until mid-exponential phase and treated with 0.5mM isopropyl-β-d-thiogalactopyranoside (IPTG) to induce expression of the empty vector or the small RNA. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 subst. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: delta dicF, lacIq PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba, Adhya and Crombrugge. J. Bio Chem. 1981, 256: p11905-11910 PGCGROWTHCONDITIONS
protocol: small RNA DicF PGCGROWTHCONDITIONS
Ribosomal RNA was removed from 1 μg of total RNA using Ribozero rRNA Removal Meta-Bacteria Kit (Epicentre Biotechnologies) and the mRNA-enriched fraction was converted to indexed RNA-seq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel formatted matrix table containing transcript coordinates, normalized abundance estimates across the biological replicates and fold-changes in gene expression between cells expressing Vector and DicF. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed-VectorvsDicF-operon.txt: .txt tab delimited file with operons expressed differently between vector and DicF PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed-VectorvsDicF-transcripts.txt: .txt raw output file from Rockhopper PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed-VectorvsDicF-transcripts.xlsx: Excel file with transcription start and stop, expression values of all genes in the E. coli genome in vector and DicF PGCGROWTHCONDITIONS
The program Rockhopper (described in Mc Clure, et al. Nucleic Acids Research. 2013, 41(14)) was used for alignment, normalization, and quantification. Genome_builg: K-12 subst. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
DicF rep2 PGCGROWTHCONDITIONS
E. coli cells were grown in Luria Broth supplemented with 100ug/ml ampicillin to retain the plasmids. PGCGROWTHCONDITIONS
E. coli cells were grown until mid-exponential phase and treated with 0.5mM isopropyl-β-d-thiogalactopyranoside (IPTG) to induce expression of the empty vector or the small RNA. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 subst. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: delta dicF, lacIq PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba, Adhya and Crombrugge. J. Bio Chem. 1981, 256: p11905-11910 PGCGROWTHCONDITIONS
protocol: small RNA DicF PGCGROWTHCONDITIONS
Ribosomal RNA was removed from 1 μg of total RNA using Ribozero rRNA Removal Meta-Bacteria Kit (Epicentre Biotechnologies) and the mRNA-enriched fraction was converted to indexed RNA-seq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel formatted matrix table containing transcript coordinates, normalized abundance estimates across the biological replicates and fold-changes in gene expression between cells expressing Vector and DicF. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed-VectorvsDicF-operon.txt: .txt tab delimited file with operons expressed differently between vector and DicF PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed-VectorvsDicF-transcripts.txt: .txt raw output file from Rockhopper PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed-VectorvsDicF-transcripts.xlsx: Excel file with transcription start and stop, expression values of all genes in the E. coli genome in vector and DicF PGCGROWTHCONDITIONS
The program Rockhopper (described in Mc Clure, et al. Nucleic Acids Research. 2013, 41(14)) was used for alignment, normalization, and quantification. Genome_builg: K-12 subst. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
DicF rep3 PGCGROWTHCONDITIONS
E. coli cells were grown in Luria Broth supplemented with 100ug/ml ampicillin to retain the plasmids. PGCGROWTHCONDITIONS
E. coli cells were grown until mid-exponential phase and treated with 0.5mM isopropyl-β-d-thiogalactopyranoside (IPTG) to induce expression of the empty vector or the small RNA. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: K-12 subst. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
genotype: delta dicF, lacIq PGCGROWTHCONDITIONS
Hot phenol RNA extraction as described in Aiba, Adhya and Crombrugge. J. Bio Chem. 1981, 256: p11905-11910 PGCGROWTHCONDITIONS
protocol: small RNA DicF PGCGROWTHCONDITIONS
Ribosomal RNA was removed from 1 μg of total RNA using Ribozero rRNA Removal Meta-Bacteria Kit (Epicentre Biotechnologies) and the mRNA-enriched fraction was converted to indexed RNA-seq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel formatted matrix table containing transcript coordinates, normalized abundance estimates across the biological replicates and fold-changes in gene expression between cells expressing Vector and DicF. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed-VectorvsDicF-operon.txt: .txt tab delimited file with operons expressed differently between vector and DicF PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed-VectorvsDicF-transcripts.txt: .txt raw output file from Rockhopper PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Processed-VectorvsDicF-transcripts.xlsx: Excel file with transcription start and stop, expression values of all genes in the E. coli genome in vector and DicF PGCGROWTHCONDITIONS
The program Rockhopper (described in Mc Clure, et al. Nucleic Acids Research. 2013, 41(14)) was used for alignment, normalization, and quantification. Genome_builg: K-12 subst. MG1655 genome (NC_000913.3)/ASM584v1 PGCGROWTHCONDITIONS
Total RNA from bacterial culture PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
MG1655 chemostat PGCGROWTHCONDITIONS
MG1655 transcriptome from chemostat growth_1 PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K12 (MG1655) PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: chemostat growth PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
MG1655 batch PGCGROWTHCONDITIONS
MG1655 transcriptome from batch growth_1 PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K12 (MG1655) PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: batch growth PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
MG1655 starvation PGCGROWTHCONDITIONS
MG1655 transcriptome from starvation growth_1 PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K12 (MG1655) PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: starvation growth PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
IAI1 chemostat PGCGROWTHCONDITIONS
IAI1 transcriptome from chemostat growth_1 PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: IAI1 PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: chemostat growth PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
IAI1 batch PGCGROWTHCONDITIONS
IAI1 transcriptome from batch growth_1 PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: IAI1 PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: batch growth PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
IAI1 starvation PGCGROWTHCONDITIONS
IAI1 transcriptome from starvation growth_1 PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: IAI1 PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: starvation growth PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: TW11588 PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: chemostat growth PGCGROWTHCONDITIONS
TW11588 chemostat PGCGROWTHCONDITIONS
TW11588 transcriptome from chemostat growth_1 PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: TW11588 PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: batch growth PGCGROWTHCONDITIONS
TW11588 batch PGCGROWTHCONDITIONS
TW11588 transcriptome from batch growth_1 PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: TW11588 PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: starvation growth PGCGROWTHCONDITIONS
TW11588 starvation PGCGROWTHCONDITIONS
TW11588 transcriptome from starvation growth_1 PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: TW09308 PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: chemostat growth PGCGROWTHCONDITIONS
TW09308 chemostat PGCGROWTHCONDITIONS
TW09308 transcriptome from chemostat growth_1 PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: TW09308 PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: batch growth PGCGROWTHCONDITIONS
TW09308 batch PGCGROWTHCONDITIONS
TW09308 transcriptome from batch growth_1 PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: TW09308 PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: starvation growth PGCGROWTHCONDITIONS
TW09308 starvation PGCGROWTHCONDITIONS
TW09308 transcriptome from starvation growth_1 PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
MG1655 chemostat PGCGROWTHCONDITIONS
MG1655 transcriptome from chemostat growth_2 PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K12 (MG1655) PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: chemostat growth PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
MG1655 batch PGCGROWTHCONDITIONS
MG1655 transcriptome from batch growth_2 PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K12 (MG1655) PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: batch growth PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
MG1655 starvation PGCGROWTHCONDITIONS
MG1655 transcriptome from starvation growth_2 PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K12 (MG1655) PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: starvation growth PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
IAI1 chemostat PGCGROWTHCONDITIONS
IAI1 transcriptome from chemostat growth_2 PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: IAI1 PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: chemostat growth PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
IAI1 batch PGCGROWTHCONDITIONS
IAI1 transcriptome from batch growth_2 PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: IAI1 PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: batch growth PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
IAI1 starvation PGCGROWTHCONDITIONS
IAI1 transcriptome from starvation growth_2 PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: IAI1 PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: starvation growth PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: TW11588 PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: chemostat growth PGCGROWTHCONDITIONS
TW11588 chemostat PGCGROWTHCONDITIONS
TW11588 transcriptome from chemostat growth_2 PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: TW11588 PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: batch growth PGCGROWTHCONDITIONS
TW11588 batch PGCGROWTHCONDITIONS
TW11588 transcriptome from batch growth_2 PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: TW11588 PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: starvation growth PGCGROWTHCONDITIONS
TW11588 starvation PGCGROWTHCONDITIONS
TW11588 transcriptome from starvation growth_2 PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: TW09308 PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: chemostat growth PGCGROWTHCONDITIONS
TW09308 chemostat PGCGROWTHCONDITIONS
TW09308 transcriptome from chemostat growth_2 PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: TW09308 PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: batch growth PGCGROWTHCONDITIONS
TW09308 batch PGCGROWTHCONDITIONS
TW09308 transcriptome from batch growth_2 PGCGROWTHCONDITIONS
A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC. PGCGROWTHCONDITIONS
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588) PGCGROWTHCONDITIONS
growth protocol: Bacteria liquid culture PGCGROWTHCONDITIONS
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions. PGCGROWTHCONDITIONS
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best) PGCGROWTHCONDITIONS
Quality trimming of 3' end at Read Segment Quality Control Indicator. PGCGROWTHCONDITIONS
Remove non-protein coding counts PGCGROWTHCONDITIONS
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: TW09308 PGCGROWTHCONDITIONS
Summarize the read count to each annotated gene PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes) PGCGROWTHCONDITIONS
treatment: starvation growth PGCGROWTHCONDITIONS
TW09308 starvation PGCGROWTHCONDITIONS
TW09308 transcriptome from starvation growth_2 PGCGROWTHCONDITIONS
All cultures were based on MOPS media with 0.2% glucose (Teknova), with full supplement (Neidhardt et al., 1974) minus methionine. An overnight liquid culture was diluted 400-fold into 200 ml fresh media. The culture was kept in a 1 liter flask at 37°C with aeration until OD420 reached 0.4. PGCGROWTHCONDITIONS
bacteria PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described previously (Li et al., 2012; Oh et al., 2011). For ribosome profiling, 200 mL of cell culture were filtered rapidly and the resulting cell pellet was flash-frozen in liquid nitrogen and combined with 650 µL of frozen lysis buffer (10 mM MgCl2, 100mM NH4Cl, 20mM Tris-HCl pH 8.0, 0.1% Nonidet P40, 0.4% Triton X-100, 100 U/mL DNase I (Roche), 1mM chloramphenicol). Cells were pulverized in 10mL canisters pre-chilled in liquid nitrogen. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. For mRNA-seq and DMS-seq, cells were pelleted by centrifuging for 2 min at 8000rpm. Total RNA was then hot acid phenol extracted. Ribosomal RNA and small RNA were removed with MICROBExpress (Ambion) or Ribozero (Epicenter) and MEGAclear (Ambion), respectively. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of exponentially growing E. coli were incubated with 750 µL DMS for 2 min at 37°C. For kasugamycin (ksg) experiments, ksg was added to a final concentration of 10 mg/mL to ΔgcvB cells for 2 min at 37°C prior to DMS modification. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol). For in vitro DMS modifications, mRNA was denatured at 95 °C for 2 min, cooled on ice and refolded in 90 µL RNA folding buffer (10 mM Tris pH 8.0, 100 mM NaCl, 6 mM MgCl2) at 37°C for 30 min then incubated in either .2% DMS for 1 min (95°C) or 4% DMS for 5 min (37°C). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
mRNA-seq 37°C in WT with control plasmid PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain: MG1655 [p-CTRL] PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
The ribosome footprints and fragmented mRNA were ligated to miRNA cloning linker-1 (IDT) using truncated T4 RNA ligase 2 K227Q. The ligated RNA fragments were reverse transribed using the primer 5Phos/GATCGTCGGACTGTAGAACTCTGAACCTGTCGGTGGTCGCC GTATCATT/iSp18/CACTCA/iSp18/CAAGCAGAAGACGGCATACGAATTGATG GTGCCTACAG. The resulting cDNA was circularized with CircLigase (Epicentre) and PCR amplification was done as described previously (Ingolia et al., 2009). PGCGROWTHCONDITIONS
treatment: 1mM IPTG PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All cultures were based on MOPS media with 0.2% glucose (Teknova), with full supplement (Neidhardt et al., 1974) minus methionine. An overnight liquid culture was diluted 400-fold into 200 ml fresh media. The culture was kept in a 1 liter flask at 37°C with aeration until OD420 reached 0.4. PGCGROWTHCONDITIONS
bacteria PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described previously (Li et al., 2012; Oh et al., 2011). For ribosome profiling, 200 mL of cell culture were filtered rapidly and the resulting cell pellet was flash-frozen in liquid nitrogen and combined with 650 µL of frozen lysis buffer (10 mM MgCl2, 100mM NH4Cl, 20mM Tris-HCl pH 8.0, 0.1% Nonidet P40, 0.4% Triton X-100, 100 U/mL DNase I (Roche), 1mM chloramphenicol). Cells were pulverized in 10mL canisters pre-chilled in liquid nitrogen. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. For mRNA-seq and DMS-seq, cells were pelleted by centrifuging for 2 min at 8000rpm. Total RNA was then hot acid phenol extracted. Ribosomal RNA and small RNA were removed with MICROBExpress (Ambion) or Ribozero (Epicenter) and MEGAclear (Ambion), respectively. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of exponentially growing E. coli were incubated with 750 µL DMS for 2 min at 37°C. For kasugamycin (ksg) experiments, ksg was added to a final concentration of 10 mg/mL to ΔgcvB cells for 2 min at 37°C prior to DMS modification. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol). For in vitro DMS modifications, mRNA was denatured at 95 °C for 2 min, cooled on ice and refolded in 90 µL RNA folding buffer (10 mM Tris pH 8.0, 100 mM NaCl, 6 mM MgCl2) at 37°C for 30 min then incubated in either .2% DMS for 1 min (95°C) or 4% DMS for 5 min (37°C). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUA PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain: MG1655 [p-CUA] PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
The ribosome footprints and fragmented mRNA were ligated to miRNA cloning linker-1 (IDT) using truncated T4 RNA ligase 2 K227Q. The ligated RNA fragments were reverse transribed using the primer 5Phos/GATCGTCGGACTGTAGAACTCTGAACCTGTCGGTGGTCGCC GTATCATT/iSp18/CACTCA/iSp18/CAAGCAGAAGACGGCATACGAATTGATG GTGCCTACAG. The resulting cDNA was circularized with CircLigase (Epicentre) and PCR amplification was done as described previously (Ingolia et al., 2009). PGCGROWTHCONDITIONS
treatment: 1mM IPTG PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
All cultures were based on MOPS media with 0.2% glucose (Teknova), with full supplement (Neidhardt et al., 1974) minus methionine. An overnight liquid culture was diluted 400-fold into 200 ml fresh media. The culture was kept in a 1 liter flask at 37°C with aeration until OD420 reached 0.4. PGCGROWTHCONDITIONS
bacteria PGCGROWTHCONDITIONS
Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Extraction was performed as described previously (Li et al., 2012; Oh et al., 2011). For ribosome profiling, 200 mL of cell culture were filtered rapidly and the resulting cell pellet was flash-frozen in liquid nitrogen and combined with 650 µL of frozen lysis buffer (10 mM MgCl2, 100mM NH4Cl, 20mM Tris-HCl pH 8.0, 0.1% Nonidet P40, 0.4% Triton X-100, 100 U/mL DNase I (Roche), 1mM chloramphenicol). Cells were pulverized in 10mL canisters pre-chilled in liquid nitrogen. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. For mRNA-seq and DMS-seq, cells were pelleted by centrifuging for 2 min at 8000rpm. Total RNA was then hot acid phenol extracted. Ribosomal RNA and small RNA were removed with MICROBExpress (Ambion) or Ribozero (Epicenter) and MEGAclear (Ambion), respectively. PGCGROWTHCONDITIONS
For in vivo DMS modification, 15 mL of exponentially growing E. coli were incubated with 750 µL DMS for 2 min at 37°C. For kasugamycin (ksg) experiments, ksg was added to a final concentration of 10 mg/mL to ΔgcvB cells for 2 min at 37°C prior to DMS modification. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol). For in vitro DMS modifications, mRNA was denatured at 95 °C for 2 min, cooled on ice and refolded in 90 µL RNA folding buffer (10 mM Tris pH 8.0, 100 mM NaCl, 6 mM MgCl2) at 37°C for 30 min then incubated in either .2% DMS for 1 min (95°C) or 4% DMS for 5 min (37°C). PGCGROWTHCONDITIONS
Genome_build: NC000913.2 PGCGROWTHCONDITIONS
mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUG PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
strain: MG1655 [p-CUG] PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
The ribosome footprints and fragmented mRNA were ligated to miRNA cloning linker-1 (IDT) using truncated T4 RNA ligase 2 K227Q. The ligated RNA fragments were reverse transribed using the primer 5Phos/GATCGTCGGACTGTAGAACTCTGAACCTGTCGGTGGTCGCC GTATCATT/iSp18/CACTCA/iSp18/CAAGCAGAAGACGGCATACGAATTGATG GTGCCTACAG. The resulting cDNA was circularized with CircLigase (Epicentre) and PCR amplification was done as described previously (Ingolia et al., 2009). PGCGROWTHCONDITIONS
treatment: 1mM IPTG PGCGROWTHCONDITIONS
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
5' linker and poly A-tail removal using READemption PGCGROWTHCONDITIONS
5 ml of cell suspension were added to 0.625 ml of pre-chilled stop solution (5 % phenol/95 % ethanol), vortexed and incubated for 5 min on ice. Cells were pelleted for 5 min at 5000 g, flash frozen in a dry ice-ethanol bath and stored at -80oC. PGCGROWTHCONDITIONS
An overnight culture of E. coli O104:H4 strain LB226692 was diluted 1:10,000 in pre-warmed LB medium (10 g/L tryptone, 5 g/L yeast extract, 5 g/L NaCl) and cells were grown at 37oC, 180 rpm for 3.5 h to an OD600 of 0.52. PGCGROWTHCONDITIONS
cDNA libraries for the Illumina sequencing platform were constructed by vertis Biotechnology AG, Germany, as described previously (Berezikov et al.,2006), without the RNA size-fractionation step prior to cDNA synthesis. Briefly, RNA samples were polyA-tailed using polyA polymerase. Then, the 5'-PPP termini were converted to 5'-P using tobacco acid pyrophosphatase (TAP) to allow for the ligation of the 5’ end RNA adapter. First-strand cDNA was synthesized by an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. In a PCR-based amplification step using a high fidelity DNA polymerase the cDNA concentration was increased to 20-30 ng/µl. A library-specific barcode for multiplex sequencing was part of a 3'-sequencing adapter. PGCGROWTHCONDITIONS
Escherichia coli O104:H4 PGCGROWTHCONDITIONS
exponentially growing cells PGCGROWTHCONDITIONS
FastQ quality trimming using FastX (version 0.0.13)  and a cut-off value of 20 PGCGROWTHCONDITIONS
Fastq to fasta conversion using FastX  FastX (version 0.0.13) PGCGROWTHCONDITIONS
generation of coverage graphs representing the number of pAA plasmid-associated mapped reads per nucleotide using READemption 0.3.7 PGCGROWTHCONDITIONS
Genome_build: NC_018658.1, NC_018659.1, NC_018660.1, NC_018666.1 PGCGROWTHCONDITIONS
mapping of non-rRNA and tRNA reads to E. coli O104:H4 chromosome and plasmids using READemption 0.3.7 and segemehl 0.2.0 PGCGROWTHCONDITIONS
mapping of reads to E. coli O104:H4 rRNAs and tRNAs using READemption 0.3.7 and segemehl 0.2.0 PGCGROWTHCONDITIONS
normalization of graphs to the total number of mapped reads per library using READemption 0.3.7 PGCGROWTHCONDITIONS
origin of isolation: patient with hemolytic uremic syndrome (HUS) PGCGROWTHCONDITIONS
outbreak: 2011 outbreak centered in Northern Germany PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: clinical isolate LB226692 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wig files representing the normalized number of pAA-associated mapped reads per nucleotide. Files contain wiggle-formatted files data for accessions  NC_018658.1, NC_018659.1, NC_018660.1, and NC_018666.1. PGCGROWTHCONDITIONS
TEX-_E. coli O104:H4 PGCGROWTHCONDITIONS
Total RNA was extracted using the Trizol reagent (Thermo Fisher Scientific) and the concentration and purity of the samples were determined using Nano Drop. RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation. gDNA was removed by Turbo DNase (Thermo Fisher Scientific) in the presence of 1U/L RiboLock RNase Inhibitor (Thermo Fisher Scientific) for 60 min at 37°C. Following organic extraction (1x 25:24:1 v/v phenol/chloroform/ isoamyalcohol, 1x chloroform), RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate (pH 5.2). Next, the sample (TEX+) was depleted of processed RNAs using 1U per 1μg of RNA Terminator 5´-Phosphate-Dependent Exonuclease (TEX, Epicentre) in the presence of 1U/μL RNase Inhibitor for 60 min at 30° C. A control reaction without TEX (TEX-) was run in parallel. Following organic extraction, RNA was recovered by overnight precipitation and resuspended in RNase-free water. PGCGROWTHCONDITIONS
5' linker and poly A-tail removal using READemption PGCGROWTHCONDITIONS
5 ml of cell suspension were added to 0.625 ml of pre-chilled stop solution (5 % phenol/95 % ethanol), vortexed and incubated for 5 min on ice. Cells were pelleted for 5 min at 5000 g, flash frozen in a dry ice-ethanol bath and stored at -80oC. PGCGROWTHCONDITIONS
An overnight culture of E. coli O104:H4 strain LB226692 was diluted 1:10,000 in pre-warmed LB medium (10 g/L tryptone, 5 g/L yeast extract, 5 g/L NaCl) and cells were grown at 37oC, 180 rpm for 3.5 h to an OD600 of 0.52. PGCGROWTHCONDITIONS
cDNA libraries for the Illumina sequencing platform were constructed by vertis Biotechnology AG, Germany, as described previously (Berezikov et al.,2006), without the RNA size-fractionation step prior to cDNA synthesis. Briefly, RNA samples were polyA-tailed using polyA polymerase. Then, the 5'-PPP termini were converted to 5'-P using tobacco acid pyrophosphatase (TAP) to allow for the ligation of the 5’ end RNA adapter. First-strand cDNA was synthesized by an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. In a PCR-based amplification step using a high fidelity DNA polymerase the cDNA concentration was increased to 20-30 ng/µl. A library-specific barcode for multiplex sequencing was part of a 3'-sequencing adapter. PGCGROWTHCONDITIONS
Escherichia coli O104:H4 PGCGROWTHCONDITIONS
exponentially growing cells PGCGROWTHCONDITIONS
FastQ quality trimming using FastX (version 0.0.13)  and a cut-off value of 20 PGCGROWTHCONDITIONS
Fastq to fasta conversion using FastX  FastX (version 0.0.13) PGCGROWTHCONDITIONS
generation of coverage graphs representing the number of pAA plasmid-associated mapped reads per nucleotide using READemption 0.3.7 PGCGROWTHCONDITIONS
Genome_build: NC_018658.1, NC_018659.1, NC_018660.1, NC_018666.1 PGCGROWTHCONDITIONS
mapping of non-rRNA and tRNA reads to E. coli O104:H4 chromosome and plasmids using READemption 0.3.7 and segemehl 0.2.0 PGCGROWTHCONDITIONS
mapping of reads to E. coli O104:H4 rRNAs and tRNAs using READemption 0.3.7 and segemehl 0.2.0 PGCGROWTHCONDITIONS
normalization of graphs to the total number of mapped reads per library using READemption 0.3.7 PGCGROWTHCONDITIONS
origin of isolation: patient with hemolytic uremic syndrome (HUS) PGCGROWTHCONDITIONS
outbreak: 2011 outbreak centered in Northern Germany PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: clinical isolate LB226692 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: wig files representing the normalized number of pAA-associated mapped reads per nucleotide. Files contain wiggle-formatted files data for accessions  NC_018658.1, NC_018659.1, NC_018660.1, and NC_018666.1. PGCGROWTHCONDITIONS
TEX+_E. coli O104:H4 PGCGROWTHCONDITIONS
Total RNA was extracted using the Trizol reagent (Thermo Fisher Scientific) and the concentration and purity of the samples were determined using Nano Drop. RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation. gDNA was removed by Turbo DNase (Thermo Fisher Scientific) in the presence of 1U/L RiboLock RNase Inhibitor (Thermo Fisher Scientific) for 60 min at 37°C. Following organic extraction (1x 25:24:1 v/v phenol/chloroform/ isoamyalcohol, 1x chloroform), RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate (pH 5.2). Next, the sample (TEX+) was depleted of processed RNAs using 1U per 1μg of RNA Terminator 5´-Phosphate-Dependent Exonuclease (TEX, Epicentre) in the presence of 1U/μL RNase Inhibitor for 60 min at 30° C. A control reaction without TEX (TEX-) was run in parallel. Following organic extraction, RNA was recovered by overnight precipitation and resuspended in RNase-free water. PGCGROWTHCONDITIONS
Cells were harvested from aerobic and anaerobic cultures of seven E. coli strains grown to an OD600 of 0.6 (exponential phase). Cultures were divided into 10 ml aliquots and were immediately mixed with 0.2 volumes of ice-cold STOP solution (95% ethanol, 5% phenol (pH 4.7)). After 20 min incubation on ice, samples were spun down for 10 min at 4˚C and 7000 x g in a centrifuge. Pellets from one aliquot were gently resuspended in RNAProtect (QIAGEN, Germany) to further stabilize the RNA. Remaining samples were mixed with RNAlater (QIAGEN, Germany) and placed at -80˚C for archival storage. Total RNA was extracted using RNeasy Mini kit (QIAGEN, Germany) and on column DNase treatment following the manufacturers’ instructions. The 23S and 16S rRNAs were removed by subtractive hybridization using the MICROBExpress kit (Ambion, USA) with modifications. Compared with the standard protocol, 50% more capture oligonucleotides and magnetic beads were used. 5S rRNAs (120 nt in length) were removed during the total RNA extraction on column. Specifically, ribosomal depletion on total RNA isolated from the E. coli BL21 (DE3) was performed using RiboZero (Gram Negative Bacteria) kit (Epicenter, USA). RNA samples were stored at -80°C. PGCGROWTHCONDITIONS
Crooks_aero PGCGROWTHCONDITIONS
Crooks_aero PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli strains E.coli C (DSMZ 4860), E. coli Crooks (DSMZ 1576), E. coli DH5α (DSMZ 6897) E. coli W (DSMZ 1116), E. coli W3110 (DSMZ 5911) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures; E. coli BL21 (DE3) was purchased as competent cells from Agilent (Agilent Technologies Inc., USA), E. coli K-12 MG1655 (ATCC 700926). All strains were cultured in M9 minimal medium (1) containing Na2HPO4 x 7H2O (6.8 g), KH2PO4 (3 g), NaCl (0.5 g), NH4Cl (1 g), MgSO4 (2 mmol), CaCl2 (0.1 mmol), trace elements, Wolf’s vitamin solution (2) and glucose (2 g L-1). Anoxic M9 minimal media with glucose was obtained by flushing solution with oxygen free nitrogen (95%). Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density (OD600) of 0.01. Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml glucose-M9 minimal media in a shaking incubator at 37°C and 250 rpm. PGCGROWTHCONDITIONS
Gene expression data (3 biological replicates per strain) were analyzed in the statistical software program R (www.r-project.org ) using the EdgeR package (3). Data were normalized using the CQN package, which accounts for both gene length and GC content effects (4). Differentially expressed genes were determined by comparing expression values under anaerobic and aerobic conditions. Those genes with adjusted P values less than 0.01 (i.e., false discovery rate less than 1%) were identified as significantly differentially expressed genes. Finally, gene annotations were automatically made using the biomaRt package (5) together with the annotation files available at the Ensembl database (www.ensembl.org) and gene set enrichment analysis (GSEA) was performed using the piano package (6). All R packages used in this study are available in Bioconductor (www.bioconductor.org). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: Crooks PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include gene expresion values for each Sample PGCGROWTHCONDITIONS
The sequencing libraries were constructed using the TruSeq RNA Sample Preparation kit (Illumina Inc., USA). Each library was prepared with RNA isolated from seven E. coli cultures grown in triplicate to an exponential phase under aerobic and anaerobic conditions. RT-PCR was performed with SuperScript® II One-step RT-PCR reagents (Invitrogen, USA). The libraries were sequenced using the Illumina HiSeq2000 platform with a paired-end protocol and read lengths of 50 nt.  The final concentration of DNA and RNA was measured using a Qubit 2.0 Fluorometer (Invitrogen, USA). The integrity of total RNA, DNA contamination, removal of rRNAs and cDNA library validation were assessed with Agilent 2100 Bioanalyzer (Agilent Technologies, USA). PGCGROWTHCONDITIONS
Cells were harvested from aerobic and anaerobic cultures of seven E. coli strains grown to an OD600 of 0.6 (exponential phase). Cultures were divided into 10 ml aliquots and were immediately mixed with 0.2 volumes of ice-cold STOP solution (95% ethanol, 5% phenol (pH 4.7)). After 20 min incubation on ice, samples were spun down for 10 min at 4˚C and 7000 x g in a centrifuge. Pellets from one aliquot were gently resuspended in RNAProtect (QIAGEN, Germany) to further stabilize the RNA. Remaining samples were mixed with RNAlater (QIAGEN, Germany) and placed at -80˚C for archival storage. Total RNA was extracted using RNeasy Mini kit (QIAGEN, Germany) and on column DNase treatment following the manufacturers’ instructions. The 23S and 16S rRNAs were removed by subtractive hybridization using the MICROBExpress kit (Ambion, USA) with modifications. Compared with the standard protocol, 50% more capture oligonucleotides and magnetic beads were used. 5S rRNAs (120 nt in length) were removed during the total RNA extraction on column. Specifically, ribosomal depletion on total RNA isolated from the E. coli BL21 (DE3) was performed using RiboZero (Gram Negative Bacteria) kit (Epicenter, USA). RNA samples were stored at -80°C. PGCGROWTHCONDITIONS
Crooks_anaero PGCGROWTHCONDITIONS
Crooks_anaero PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli strains E.coli C (DSMZ 4860), E. coli Crooks (DSMZ 1576), E. coli DH5α (DSMZ 6897) E. coli W (DSMZ 1116), E. coli W3110 (DSMZ 5911) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures; E. coli BL21 (DE3) was purchased as competent cells from Agilent (Agilent Technologies Inc., USA), E. coli K-12 MG1655 (ATCC 700926). All strains were cultured in M9 minimal medium (1) containing Na2HPO4 x 7H2O (6.8 g), KH2PO4 (3 g), NaCl (0.5 g), NH4Cl (1 g), MgSO4 (2 mmol), CaCl2 (0.1 mmol), trace elements, Wolf’s vitamin solution (2) and glucose (2 g L-1). Anoxic M9 minimal media with glucose was obtained by flushing solution with oxygen free nitrogen (95%). Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density (OD600) of 0.01. Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml glucose-M9 minimal media in a shaking incubator at 37°C and 250 rpm. PGCGROWTHCONDITIONS
Gene expression data (3 biological replicates per strain) were analyzed in the statistical software program R (www.r-project.org ) using the EdgeR package (3). Data were normalized using the CQN package, which accounts for both gene length and GC content effects (4). Differentially expressed genes were determined by comparing expression values under anaerobic and aerobic conditions. Those genes with adjusted P values less than 0.01 (i.e., false discovery rate less than 1%) were identified as significantly differentially expressed genes. Finally, gene annotations were automatically made using the biomaRt package (5) together with the annotation files available at the Ensembl database (www.ensembl.org) and gene set enrichment analysis (GSEA) was performed using the piano package (6). All R packages used in this study are available in Bioconductor (www.bioconductor.org). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: Crooks PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include gene expresion values for each Sample PGCGROWTHCONDITIONS
The sequencing libraries were constructed using the TruSeq RNA Sample Preparation kit (Illumina Inc., USA). Each library was prepared with RNA isolated from seven E. coli cultures grown in triplicate to an exponential phase under aerobic and anaerobic conditions. RT-PCR was performed with SuperScript® II One-step RT-PCR reagents (Invitrogen, USA). The libraries were sequenced using the Illumina HiSeq2000 platform with a paired-end protocol and read lengths of 50 nt.  The final concentration of DNA and RNA was measured using a Qubit 2.0 Fluorometer (Invitrogen, USA). The integrity of total RNA, DNA contamination, removal of rRNAs and cDNA library validation were assessed with Agilent 2100 Bioanalyzer (Agilent Technologies, USA). PGCGROWTHCONDITIONS
carbon source: glycerol PGCGROWTHCONDITIONS
Cells were grown at 37°C in M4 minimal medium under oxic and anoxic conditions. The minimal medium (1.27 mM K2HPO4, 0.73 mM KH2PO4, 5 mM sodium HEPES, 150 mM NaCl, 9 mM (NH4)2SO4) was supplemented with 0.1 g/l caseinhydrolysate 1 mM MgSO4, 0.1 mM CaCl2 and trace elements (5 μM CoCl2, 0.2 μM CuSO4, 57 μM H3BO3, 5.4 μM FeCl2, 1.3 μM MnSO4, 67.2 μM Na2EDTA, 3.9 μM Na2MoO4, 1.5 μM Na2SeO4, 5 μM NiCl2, and 1 μM ZnSO4). The pH of the media was adjusted to 7.2. Glycerol (50 mM) or glycerol (50mM) plus propionate (10 mM) served as the carbon and electron sources, respectively. Potassium nitrate (50 mM) was the electron acceptor under anoxic conditions. PGCGROWTHCONDITIONS
Cluster detection and base calling were performed using RTA v1.13 (Illumina), and the quality of the reads was assessed with CASAVA v1.8.1 (Illumina). PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Gene expression was calculated as reads per gene by determining the number of reads that overlapped with the annotated gene loci using HTSeq (Anders et al., 2015, doi: 10.1093/bioinformatics/btu638) with the option 'intersection-nonempty'. PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 E. coli K12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: K-12 wild type PGCGROWTHCONDITIONS
molecule subtype: total RNA (ribosome-depleted) PGCGROWTHCONDITIONS
No further treatment was applied. PGCGROWTHCONDITIONS
oxic/anoxic: anoxic (NO3) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Strand-specific cDNA libraries were prepared from 50 ng of rRNA-depleted samples following the TruSeq RNA protocol (Illumina, San Diego, CA, USA, without purification) with modification of the 2nd strand cDNA synthesis as previously described (Parkhomchuk et al. 2009). The libraries were prepared using multiplex primers to allow simultaneous sequencing in a single lane. Sequencing was performed on a HiSeq1500 using SBS v3 kits (Illumina) to generate paired-end reads of 2 x 50 nucleotides. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPG (reads per gene) files were created using HTSeq, mapping raw reads (fastq format) against the E. coli K12 genome and using a GFF file derived from the annotation of NC_000913.3 available from NCBI. PGCGROWTHCONDITIONS
The sequence data were mapped against the genome sequence of E. coli K12 substr. MG1655 (NCBI accession number NC_000913.3) using Bowtie2 (Langmead and Salzberg, 2012, doi:10.1038/nmeth.1923). PGCGROWTHCONDITIONS
Total RNA was isolated with the RNeasy Protect Bacteria Mini Kit from Qiagen (Hilden, Germany). The isolated RNA was further purified from genomic DNA contaminations using Ambion DNase I treatment following the manufacturer's instructions (DNA-free, Ambion by Life Technologies, Darmstadt, Germany). RNA samples were further subjected to an mRNA enrichment step using the MICROBExpress Kit from Ambion according to the manufacturer`s instructions (Life Technologies, Darmstadt, Germany). PGCGROWTHCONDITIONS
wild type_anoxic (NO3)_glycerol PGCGROWTHCONDITIONS
WT NO3 1 PGCGROWTHCONDITIONS
carbon source: glycerol PGCGROWTHCONDITIONS
Cells were grown at 37°C in M4 minimal medium under oxic and anoxic conditions. The minimal medium (1.27 mM K2HPO4, 0.73 mM KH2PO4, 5 mM sodium HEPES, 150 mM NaCl, 9 mM (NH4)2SO4) was supplemented with 0.1 g/l caseinhydrolysate 1 mM MgSO4, 0.1 mM CaCl2 and trace elements (5 μM CoCl2, 0.2 μM CuSO4, 57 μM H3BO3, 5.4 μM FeCl2, 1.3 μM MnSO4, 67.2 μM Na2EDTA, 3.9 μM Na2MoO4, 1.5 μM Na2SeO4, 5 μM NiCl2, and 1 μM ZnSO4). The pH of the media was adjusted to 7.2. Glycerol (50 mM) or glycerol (50mM) plus propionate (10 mM) served as the carbon and electron sources, respectively. Potassium nitrate (50 mM) was the electron acceptor under anoxic conditions. PGCGROWTHCONDITIONS
Cluster detection and base calling were performed using RTA v1.13 (Illumina), and the quality of the reads was assessed with CASAVA v1.8.1 (Illumina). PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Gene expression was calculated as reads per gene by determining the number of reads that overlapped with the annotated gene loci using HTSeq (Anders et al., 2015, doi: 10.1093/bioinformatics/btu638) with the option 'intersection-nonempty'. PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 E. coli K12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: K-12 wild type PGCGROWTHCONDITIONS
molecule subtype: total RNA (ribosome-depleted) PGCGROWTHCONDITIONS
No further treatment was applied. PGCGROWTHCONDITIONS
oxic/anoxic: anoxic (NO3) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Strand-specific cDNA libraries were prepared from 50 ng of rRNA-depleted samples following the TruSeq RNA protocol (Illumina, San Diego, CA, USA, without purification) with modification of the 2nd strand cDNA synthesis as previously described (Parkhomchuk et al. 2009). The libraries were prepared using multiplex primers to allow simultaneous sequencing in a single lane. Sequencing was performed on a HiSeq1500 using SBS v3 kits (Illumina) to generate paired-end reads of 2 x 50 nucleotides. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPG (reads per gene) files were created using HTSeq, mapping raw reads (fastq format) against the E. coli K12 genome and using a GFF file derived from the annotation of NC_000913.3 available from NCBI. PGCGROWTHCONDITIONS
The sequence data were mapped against the genome sequence of E. coli K12 substr. MG1655 (NCBI accession number NC_000913.3) using Bowtie2 (Langmead and Salzberg, 2012, doi:10.1038/nmeth.1923). PGCGROWTHCONDITIONS
Total RNA was isolated with the RNeasy Protect Bacteria Mini Kit from Qiagen (Hilden, Germany). The isolated RNA was further purified from genomic DNA contaminations using Ambion DNase I treatment following the manufacturer's instructions (DNA-free, Ambion by Life Technologies, Darmstadt, Germany). RNA samples were further subjected to an mRNA enrichment step using the MICROBExpress Kit from Ambion according to the manufacturer`s instructions (Life Technologies, Darmstadt, Germany). PGCGROWTHCONDITIONS
wild type_anoxic (NO3)_glycerol PGCGROWTHCONDITIONS
WT NO3 2 PGCGROWTHCONDITIONS
carbon source: glycerol PGCGROWTHCONDITIONS
Cells were grown at 37°C in M4 minimal medium under oxic and anoxic conditions. The minimal medium (1.27 mM K2HPO4, 0.73 mM KH2PO4, 5 mM sodium HEPES, 150 mM NaCl, 9 mM (NH4)2SO4) was supplemented with 0.1 g/l caseinhydrolysate 1 mM MgSO4, 0.1 mM CaCl2 and trace elements (5 μM CoCl2, 0.2 μM CuSO4, 57 μM H3BO3, 5.4 μM FeCl2, 1.3 μM MnSO4, 67.2 μM Na2EDTA, 3.9 μM Na2MoO4, 1.5 μM Na2SeO4, 5 μM NiCl2, and 1 μM ZnSO4). The pH of the media was adjusted to 7.2. Glycerol (50 mM) or glycerol (50mM) plus propionate (10 mM) served as the carbon and electron sources, respectively. Potassium nitrate (50 mM) was the electron acceptor under anoxic conditions. PGCGROWTHCONDITIONS
Cluster detection and base calling were performed using RTA v1.13 (Illumina), and the quality of the reads was assessed with CASAVA v1.8.1 (Illumina). PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Gene expression was calculated as reads per gene by determining the number of reads that overlapped with the annotated gene loci using HTSeq (Anders et al., 2015, doi: 10.1093/bioinformatics/btu638) with the option 'intersection-nonempty'. PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 E. coli K12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: K-12 wild type PGCGROWTHCONDITIONS
molecule subtype: total RNA (ribosome-depleted) PGCGROWTHCONDITIONS
No further treatment was applied. PGCGROWTHCONDITIONS
oxic/anoxic: oxic PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Strand-specific cDNA libraries were prepared from 50 ng of rRNA-depleted samples following the TruSeq RNA protocol (Illumina, San Diego, CA, USA, without purification) with modification of the 2nd strand cDNA synthesis as previously described (Parkhomchuk et al. 2009). The libraries were prepared using multiplex primers to allow simultaneous sequencing in a single lane. Sequencing was performed on a HiSeq1500 using SBS v3 kits (Illumina) to generate paired-end reads of 2 x 50 nucleotides. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPG (reads per gene) files were created using HTSeq, mapping raw reads (fastq format) against the E. coli K12 genome and using a GFF file derived from the annotation of NC_000913.3 available from NCBI. PGCGROWTHCONDITIONS
The sequence data were mapped against the genome sequence of E. coli K12 substr. MG1655 (NCBI accession number NC_000913.3) using Bowtie2 (Langmead and Salzberg, 2012, doi:10.1038/nmeth.1923). PGCGROWTHCONDITIONS
Total RNA was isolated with the RNeasy Protect Bacteria Mini Kit from Qiagen (Hilden, Germany). The isolated RNA was further purified from genomic DNA contaminations using Ambion DNase I treatment following the manufacturer's instructions (DNA-free, Ambion by Life Technologies, Darmstadt, Germany). RNA samples were further subjected to an mRNA enrichment step using the MICROBExpress Kit from Ambion according to the manufacturer`s instructions (Life Technologies, Darmstadt, Germany). PGCGROWTHCONDITIONS
wild type_oxic_glycerol PGCGROWTHCONDITIONS
WT O2 1 PGCGROWTHCONDITIONS
carbon source: glycerol PGCGROWTHCONDITIONS
Cells were grown at 37°C in M4 minimal medium under oxic and anoxic conditions. The minimal medium (1.27 mM K2HPO4, 0.73 mM KH2PO4, 5 mM sodium HEPES, 150 mM NaCl, 9 mM (NH4)2SO4) was supplemented with 0.1 g/l caseinhydrolysate 1 mM MgSO4, 0.1 mM CaCl2 and trace elements (5 μM CoCl2, 0.2 μM CuSO4, 57 μM H3BO3, 5.4 μM FeCl2, 1.3 μM MnSO4, 67.2 μM Na2EDTA, 3.9 μM Na2MoO4, 1.5 μM Na2SeO4, 5 μM NiCl2, and 1 μM ZnSO4). The pH of the media was adjusted to 7.2. Glycerol (50 mM) or glycerol (50mM) plus propionate (10 mM) served as the carbon and electron sources, respectively. Potassium nitrate (50 mM) was the electron acceptor under anoxic conditions. PGCGROWTHCONDITIONS
Cluster detection and base calling were performed using RTA v1.13 (Illumina), and the quality of the reads was assessed with CASAVA v1.8.1 (Illumina). PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Gene expression was calculated as reads per gene by determining the number of reads that overlapped with the annotated gene loci using HTSeq (Anders et al., 2015, doi: 10.1093/bioinformatics/btu638) with the option 'intersection-nonempty'. PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 E. coli K12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: K-12 wild type PGCGROWTHCONDITIONS
molecule subtype: total RNA (ribosome-depleted) PGCGROWTHCONDITIONS
No further treatment was applied. PGCGROWTHCONDITIONS
oxic/anoxic: oxic PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Strand-specific cDNA libraries were prepared from 50 ng of rRNA-depleted samples following the TruSeq RNA protocol (Illumina, San Diego, CA, USA, without purification) with modification of the 2nd strand cDNA synthesis as previously described (Parkhomchuk et al. 2009). The libraries were prepared using multiplex primers to allow simultaneous sequencing in a single lane. Sequencing was performed on a HiSeq1500 using SBS v3 kits (Illumina) to generate paired-end reads of 2 x 50 nucleotides. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPG (reads per gene) files were created using HTSeq, mapping raw reads (fastq format) against the E. coli K12 genome and using a GFF file derived from the annotation of NC_000913.3 available from NCBI. PGCGROWTHCONDITIONS
The sequence data were mapped against the genome sequence of E. coli K12 substr. MG1655 (NCBI accession number NC_000913.3) using Bowtie2 (Langmead and Salzberg, 2012, doi:10.1038/nmeth.1923). PGCGROWTHCONDITIONS
Total RNA was isolated with the RNeasy Protect Bacteria Mini Kit from Qiagen (Hilden, Germany). The isolated RNA was further purified from genomic DNA contaminations using Ambion DNase I treatment following the manufacturer's instructions (DNA-free, Ambion by Life Technologies, Darmstadt, Germany). RNA samples were further subjected to an mRNA enrichment step using the MICROBExpress Kit from Ambion according to the manufacturer`s instructions (Life Technologies, Darmstadt, Germany). PGCGROWTHCONDITIONS
wild type_oxic_glycerol PGCGROWTHCONDITIONS
WT O2 2 PGCGROWTHCONDITIONS
carbon source: glycerol + propionate PGCGROWTHCONDITIONS
Cells were grown at 37°C in M4 minimal medium under oxic and anoxic conditions. The minimal medium (1.27 mM K2HPO4, 0.73 mM KH2PO4, 5 mM sodium HEPES, 150 mM NaCl, 9 mM (NH4)2SO4) was supplemented with 0.1 g/l caseinhydrolysate 1 mM MgSO4, 0.1 mM CaCl2 and trace elements (5 μM CoCl2, 0.2 μM CuSO4, 57 μM H3BO3, 5.4 μM FeCl2, 1.3 μM MnSO4, 67.2 μM Na2EDTA, 3.9 μM Na2MoO4, 1.5 μM Na2SeO4, 5 μM NiCl2, and 1 μM ZnSO4). The pH of the media was adjusted to 7.2. Glycerol (50 mM) or glycerol (50mM) plus propionate (10 mM) served as the carbon and electron sources, respectively. Potassium nitrate (50 mM) was the electron acceptor under anoxic conditions. PGCGROWTHCONDITIONS
Cluster detection and base calling were performed using RTA v1.13 (Illumina), and the quality of the reads was assessed with CASAVA v1.8.1 (Illumina). PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Gene expression was calculated as reads per gene by determining the number of reads that overlapped with the annotated gene loci using HTSeq (Anders et al., 2015, doi: 10.1093/bioinformatics/btu638) with the option 'intersection-nonempty'. PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 E. coli K12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: K-12 wild type PGCGROWTHCONDITIONS
molecule subtype: total RNA (ribosome-depleted) PGCGROWTHCONDITIONS
No further treatment was applied. PGCGROWTHCONDITIONS
oxic/anoxic: anoxic (NO3) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Strand-specific cDNA libraries were prepared from 50 ng of rRNA-depleted samples following the TruSeq RNA protocol (Illumina, San Diego, CA, USA, without purification) with modification of the 2nd strand cDNA synthesis as previously described (Parkhomchuk et al. 2009). The libraries were prepared using multiplex primers to allow simultaneous sequencing in a single lane. Sequencing was performed on a HiSeq1500 using SBS v3 kits (Illumina) to generate paired-end reads of 2 x 50 nucleotides. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPG (reads per gene) files were created using HTSeq, mapping raw reads (fastq format) against the E. coli K12 genome and using a GFF file derived from the annotation of NC_000913.3 available from NCBI. PGCGROWTHCONDITIONS
The sequence data were mapped against the genome sequence of E. coli K12 substr. MG1655 (NCBI accession number NC_000913.3) using Bowtie2 (Langmead and Salzberg, 2012, doi:10.1038/nmeth.1923). PGCGROWTHCONDITIONS
Total RNA was isolated with the RNeasy Protect Bacteria Mini Kit from Qiagen (Hilden, Germany). The isolated RNA was further purified from genomic DNA contaminations using Ambion DNase I treatment following the manufacturer's instructions (DNA-free, Ambion by Life Technologies, Darmstadt, Germany). RNA samples were further subjected to an mRNA enrichment step using the MICROBExpress Kit from Ambion according to the manufacturer`s instructions (Life Technologies, Darmstadt, Germany). PGCGROWTHCONDITIONS
wild type_anoxic (NO3)_glycerol + propionate PGCGROWTHCONDITIONS
WT NO3 w/propionate 1 PGCGROWTHCONDITIONS
carbon source: glycerol + propionate PGCGROWTHCONDITIONS
Cells were grown at 37°C in M4 minimal medium under oxic and anoxic conditions. The minimal medium (1.27 mM K2HPO4, 0.73 mM KH2PO4, 5 mM sodium HEPES, 150 mM NaCl, 9 mM (NH4)2SO4) was supplemented with 0.1 g/l caseinhydrolysate 1 mM MgSO4, 0.1 mM CaCl2 and trace elements (5 μM CoCl2, 0.2 μM CuSO4, 57 μM H3BO3, 5.4 μM FeCl2, 1.3 μM MnSO4, 67.2 μM Na2EDTA, 3.9 μM Na2MoO4, 1.5 μM Na2SeO4, 5 μM NiCl2, and 1 μM ZnSO4). The pH of the media was adjusted to 7.2. Glycerol (50 mM) or glycerol (50mM) plus propionate (10 mM) served as the carbon and electron sources, respectively. Potassium nitrate (50 mM) was the electron acceptor under anoxic conditions. PGCGROWTHCONDITIONS
Cluster detection and base calling were performed using RTA v1.13 (Illumina), and the quality of the reads was assessed with CASAVA v1.8.1 (Illumina). PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Gene expression was calculated as reads per gene by determining the number of reads that overlapped with the annotated gene loci using HTSeq (Anders et al., 2015, doi: 10.1093/bioinformatics/btu638) with the option 'intersection-nonempty'. PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 E. coli K12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: K-12 wild type PGCGROWTHCONDITIONS
molecule subtype: total RNA (ribosome-depleted) PGCGROWTHCONDITIONS
No further treatment was applied. PGCGROWTHCONDITIONS
oxic/anoxic: anoxic (NO3) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Strand-specific cDNA libraries were prepared from 50 ng of rRNA-depleted samples following the TruSeq RNA protocol (Illumina, San Diego, CA, USA, without purification) with modification of the 2nd strand cDNA synthesis as previously described (Parkhomchuk et al. 2009). The libraries were prepared using multiplex primers to allow simultaneous sequencing in a single lane. Sequencing was performed on a HiSeq1500 using SBS v3 kits (Illumina) to generate paired-end reads of 2 x 50 nucleotides. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPG (reads per gene) files were created using HTSeq, mapping raw reads (fastq format) against the E. coli K12 genome and using a GFF file derived from the annotation of NC_000913.3 available from NCBI. PGCGROWTHCONDITIONS
The sequence data were mapped against the genome sequence of E. coli K12 substr. MG1655 (NCBI accession number NC_000913.3) using Bowtie2 (Langmead and Salzberg, 2012, doi:10.1038/nmeth.1923). PGCGROWTHCONDITIONS
Total RNA was isolated with the RNeasy Protect Bacteria Mini Kit from Qiagen (Hilden, Germany). The isolated RNA was further purified from genomic DNA contaminations using Ambion DNase I treatment following the manufacturer's instructions (DNA-free, Ambion by Life Technologies, Darmstadt, Germany). RNA samples were further subjected to an mRNA enrichment step using the MICROBExpress Kit from Ambion according to the manufacturer`s instructions (Life Technologies, Darmstadt, Germany). PGCGROWTHCONDITIONS
wild type_anoxic (NO3)_glycerol + propionate PGCGROWTHCONDITIONS
WT NO3 w/propionate 2 PGCGROWTHCONDITIONS
carbon source: glycerol + propionate PGCGROWTHCONDITIONS
Cells were grown at 37°C in M4 minimal medium under oxic and anoxic conditions. The minimal medium (1.27 mM K2HPO4, 0.73 mM KH2PO4, 5 mM sodium HEPES, 150 mM NaCl, 9 mM (NH4)2SO4) was supplemented with 0.1 g/l caseinhydrolysate 1 mM MgSO4, 0.1 mM CaCl2 and trace elements (5 μM CoCl2, 0.2 μM CuSO4, 57 μM H3BO3, 5.4 μM FeCl2, 1.3 μM MnSO4, 67.2 μM Na2EDTA, 3.9 μM Na2MoO4, 1.5 μM Na2SeO4, 5 μM NiCl2, and 1 μM ZnSO4). The pH of the media was adjusted to 7.2. Glycerol (50 mM) or glycerol (50mM) plus propionate (10 mM) served as the carbon and electron sources, respectively. Potassium nitrate (50 mM) was the electron acceptor under anoxic conditions. PGCGROWTHCONDITIONS
Cluster detection and base calling were performed using RTA v1.13 (Illumina), and the quality of the reads was assessed with CASAVA v1.8.1 (Illumina). PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Gene expression was calculated as reads per gene by determining the number of reads that overlapped with the annotated gene loci using HTSeq (Anders et al., 2015, doi: 10.1093/bioinformatics/btu638) with the option 'intersection-nonempty'. PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 E. coli K12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: K-12 wild type PGCGROWTHCONDITIONS
molecule subtype: total RNA (ribosome-depleted) PGCGROWTHCONDITIONS
No further treatment was applied. PGCGROWTHCONDITIONS
oxic/anoxic: oxic PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Strand-specific cDNA libraries were prepared from 50 ng of rRNA-depleted samples following the TruSeq RNA protocol (Illumina, San Diego, CA, USA, without purification) with modification of the 2nd strand cDNA synthesis as previously described (Parkhomchuk et al. 2009). The libraries were prepared using multiplex primers to allow simultaneous sequencing in a single lane. Sequencing was performed on a HiSeq1500 using SBS v3 kits (Illumina) to generate paired-end reads of 2 x 50 nucleotides. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPG (reads per gene) files were created using HTSeq, mapping raw reads (fastq format) against the E. coli K12 genome and using a GFF file derived from the annotation of NC_000913.3 available from NCBI. PGCGROWTHCONDITIONS
The sequence data were mapped against the genome sequence of E. coli K12 substr. MG1655 (NCBI accession number NC_000913.3) using Bowtie2 (Langmead and Salzberg, 2012, doi:10.1038/nmeth.1923). PGCGROWTHCONDITIONS
Total RNA was isolated with the RNeasy Protect Bacteria Mini Kit from Qiagen (Hilden, Germany). The isolated RNA was further purified from genomic DNA contaminations using Ambion DNase I treatment following the manufacturer's instructions (DNA-free, Ambion by Life Technologies, Darmstadt, Germany). RNA samples were further subjected to an mRNA enrichment step using the MICROBExpress Kit from Ambion according to the manufacturer`s instructions (Life Technologies, Darmstadt, Germany). PGCGROWTHCONDITIONS
wild type_oxic_glycerol + propionate PGCGROWTHCONDITIONS
WT O2 w/propionate 1 PGCGROWTHCONDITIONS
carbon source: glycerol + propionate PGCGROWTHCONDITIONS
Cells were grown at 37°C in M4 minimal medium under oxic and anoxic conditions. The minimal medium (1.27 mM K2HPO4, 0.73 mM KH2PO4, 5 mM sodium HEPES, 150 mM NaCl, 9 mM (NH4)2SO4) was supplemented with 0.1 g/l caseinhydrolysate 1 mM MgSO4, 0.1 mM CaCl2 and trace elements (5 μM CoCl2, 0.2 μM CuSO4, 57 μM H3BO3, 5.4 μM FeCl2, 1.3 μM MnSO4, 67.2 μM Na2EDTA, 3.9 μM Na2MoO4, 1.5 μM Na2SeO4, 5 μM NiCl2, and 1 μM ZnSO4). The pH of the media was adjusted to 7.2. Glycerol (50 mM) or glycerol (50mM) plus propionate (10 mM) served as the carbon and electron sources, respectively. Potassium nitrate (50 mM) was the electron acceptor under anoxic conditions. PGCGROWTHCONDITIONS
Cluster detection and base calling were performed using RTA v1.13 (Illumina), and the quality of the reads was assessed with CASAVA v1.8.1 (Illumina). PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Gene expression was calculated as reads per gene by determining the number of reads that overlapped with the annotated gene loci using HTSeq (Anders et al., 2015, doi: 10.1093/bioinformatics/btu638) with the option 'intersection-nonempty'. PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 E. coli K12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: K-12 wild type PGCGROWTHCONDITIONS
molecule subtype: total RNA (ribosome-depleted) PGCGROWTHCONDITIONS
No further treatment was applied. PGCGROWTHCONDITIONS
oxic/anoxic: oxic PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Strand-specific cDNA libraries were prepared from 50 ng of rRNA-depleted samples following the TruSeq RNA protocol (Illumina, San Diego, CA, USA, without purification) with modification of the 2nd strand cDNA synthesis as previously described (Parkhomchuk et al. 2009). The libraries were prepared using multiplex primers to allow simultaneous sequencing in a single lane. Sequencing was performed on a HiSeq1500 using SBS v3 kits (Illumina) to generate paired-end reads of 2 x 50 nucleotides. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPG (reads per gene) files were created using HTSeq, mapping raw reads (fastq format) against the E. coli K12 genome and using a GFF file derived from the annotation of NC_000913.3 available from NCBI. PGCGROWTHCONDITIONS
The sequence data were mapped against the genome sequence of E. coli K12 substr. MG1655 (NCBI accession number NC_000913.3) using Bowtie2 (Langmead and Salzberg, 2012, doi:10.1038/nmeth.1923). PGCGROWTHCONDITIONS
Total RNA was isolated with the RNeasy Protect Bacteria Mini Kit from Qiagen (Hilden, Germany). The isolated RNA was further purified from genomic DNA contaminations using Ambion DNase I treatment following the manufacturer's instructions (DNA-free, Ambion by Life Technologies, Darmstadt, Germany). RNA samples were further subjected to an mRNA enrichment step using the MICROBExpress Kit from Ambion according to the manufacturer`s instructions (Life Technologies, Darmstadt, Germany). PGCGROWTHCONDITIONS
wild type_oxic_glycerol + propionate PGCGROWTHCONDITIONS
WT O2 w/propionate 2 PGCGROWTHCONDITIONS
carbon source: glycerol PGCGROWTHCONDITIONS
Cells were grown at 37°C in M4 minimal medium under oxic and anoxic conditions. The minimal medium (1.27 mM K2HPO4, 0.73 mM KH2PO4, 5 mM sodium HEPES, 150 mM NaCl, 9 mM (NH4)2SO4) was supplemented with 0.1 g/l caseinhydrolysate 1 mM MgSO4, 0.1 mM CaCl2 and trace elements (5 μM CoCl2, 0.2 μM CuSO4, 57 μM H3BO3, 5.4 μM FeCl2, 1.3 μM MnSO4, 67.2 μM Na2EDTA, 3.9 μM Na2MoO4, 1.5 μM Na2SeO4, 5 μM NiCl2, and 1 μM ZnSO4). The pH of the media was adjusted to 7.2. Glycerol (50 mM) or glycerol (50mM) plus propionate (10 mM) served as the carbon and electron sources, respectively. Potassium nitrate (50 mM) was the electron acceptor under anoxic conditions. PGCGROWTHCONDITIONS
Cluster detection and base calling were performed using RTA v1.13 (Illumina), and the quality of the reads was assessed with CASAVA v1.8.1 (Illumina). PGCGROWTHCONDITIONS
delta-rnr mutant_anoxic (NO3)_glycerol PGCGROWTHCONDITIONS
d_rnr NO3 1 PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Gene expression was calculated as reads per gene by determining the number of reads that overlapped with the annotated gene loci using HTSeq (Anders et al., 2015, doi: 10.1093/bioinformatics/btu638) with the option 'intersection-nonempty'. PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 E. coli K12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: K-12 delta-rnr mutant (JW5741-1) PGCGROWTHCONDITIONS
molecule subtype: total RNA (ribosome-depleted) PGCGROWTHCONDITIONS
No further treatment was applied. PGCGROWTHCONDITIONS
oxic/anoxic: anoxic (NO3) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Strand-specific cDNA libraries were prepared from 50 ng of rRNA-depleted samples following the TruSeq RNA protocol (Illumina, San Diego, CA, USA, without purification) with modification of the 2nd strand cDNA synthesis as previously described (Parkhomchuk et al. 2009). The libraries were prepared using multiplex primers to allow simultaneous sequencing in a single lane. Sequencing was performed on a HiSeq1500 using SBS v3 kits (Illumina) to generate paired-end reads of 2 x 50 nucleotides. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPG (reads per gene) files were created using HTSeq, mapping raw reads (fastq format) against the E. coli K12 genome and using a GFF file derived from the annotation of NC_000913.3 available from NCBI. PGCGROWTHCONDITIONS
The sequence data were mapped against the genome sequence of E. coli K12 substr. MG1655 (NCBI accession number NC_000913.3) using Bowtie2 (Langmead and Salzberg, 2012, doi:10.1038/nmeth.1923). PGCGROWTHCONDITIONS
Total RNA was isolated with the RNeasy Protect Bacteria Mini Kit from Qiagen (Hilden, Germany). The isolated RNA was further purified from genomic DNA contaminations using Ambion DNase I treatment following the manufacturer's instructions (DNA-free, Ambion by Life Technologies, Darmstadt, Germany). RNA samples were further subjected to an mRNA enrichment step using the MICROBExpress Kit from Ambion according to the manufacturer`s instructions (Life Technologies, Darmstadt, Germany). PGCGROWTHCONDITIONS
carbon source: glycerol PGCGROWTHCONDITIONS
Cells were grown at 37°C in M4 minimal medium under oxic and anoxic conditions. The minimal medium (1.27 mM K2HPO4, 0.73 mM KH2PO4, 5 mM sodium HEPES, 150 mM NaCl, 9 mM (NH4)2SO4) was supplemented with 0.1 g/l caseinhydrolysate 1 mM MgSO4, 0.1 mM CaCl2 and trace elements (5 μM CoCl2, 0.2 μM CuSO4, 57 μM H3BO3, 5.4 μM FeCl2, 1.3 μM MnSO4, 67.2 μM Na2EDTA, 3.9 μM Na2MoO4, 1.5 μM Na2SeO4, 5 μM NiCl2, and 1 μM ZnSO4). The pH of the media was adjusted to 7.2. Glycerol (50 mM) or glycerol (50mM) plus propionate (10 mM) served as the carbon and electron sources, respectively. Potassium nitrate (50 mM) was the electron acceptor under anoxic conditions. PGCGROWTHCONDITIONS
Cluster detection and base calling were performed using RTA v1.13 (Illumina), and the quality of the reads was assessed with CASAVA v1.8.1 (Illumina). PGCGROWTHCONDITIONS
delta-rnr mutant_anoxic (NO3)_glycerol PGCGROWTHCONDITIONS
d_rnr NO3 2 PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Gene expression was calculated as reads per gene by determining the number of reads that overlapped with the annotated gene loci using HTSeq (Anders et al., 2015, doi: 10.1093/bioinformatics/btu638) with the option 'intersection-nonempty'. PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 E. coli K12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: K-12 delta-rnr mutant (JW5741-1) PGCGROWTHCONDITIONS
molecule subtype: total RNA (ribosome-depleted) PGCGROWTHCONDITIONS
No further treatment was applied. PGCGROWTHCONDITIONS
oxic/anoxic: anoxic (NO3) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Strand-specific cDNA libraries were prepared from 50 ng of rRNA-depleted samples following the TruSeq RNA protocol (Illumina, San Diego, CA, USA, without purification) with modification of the 2nd strand cDNA synthesis as previously described (Parkhomchuk et al. 2009). The libraries were prepared using multiplex primers to allow simultaneous sequencing in a single lane. Sequencing was performed on a HiSeq1500 using SBS v3 kits (Illumina) to generate paired-end reads of 2 x 50 nucleotides. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPG (reads per gene) files were created using HTSeq, mapping raw reads (fastq format) against the E. coli K12 genome and using a GFF file derived from the annotation of NC_000913.3 available from NCBI. PGCGROWTHCONDITIONS
The sequence data were mapped against the genome sequence of E. coli K12 substr. MG1655 (NCBI accession number NC_000913.3) using Bowtie2 (Langmead and Salzberg, 2012, doi:10.1038/nmeth.1923). PGCGROWTHCONDITIONS
Total RNA was isolated with the RNeasy Protect Bacteria Mini Kit from Qiagen (Hilden, Germany). The isolated RNA was further purified from genomic DNA contaminations using Ambion DNase I treatment following the manufacturer's instructions (DNA-free, Ambion by Life Technologies, Darmstadt, Germany). RNA samples were further subjected to an mRNA enrichment step using the MICROBExpress Kit from Ambion according to the manufacturer`s instructions (Life Technologies, Darmstadt, Germany). PGCGROWTHCONDITIONS
carbon source: glycerol PGCGROWTHCONDITIONS
Cells were grown at 37°C in M4 minimal medium under oxic and anoxic conditions. The minimal medium (1.27 mM K2HPO4, 0.73 mM KH2PO4, 5 mM sodium HEPES, 150 mM NaCl, 9 mM (NH4)2SO4) was supplemented with 0.1 g/l caseinhydrolysate 1 mM MgSO4, 0.1 mM CaCl2 and trace elements (5 μM CoCl2, 0.2 μM CuSO4, 57 μM H3BO3, 5.4 μM FeCl2, 1.3 μM MnSO4, 67.2 μM Na2EDTA, 3.9 μM Na2MoO4, 1.5 μM Na2SeO4, 5 μM NiCl2, and 1 μM ZnSO4). The pH of the media was adjusted to 7.2. Glycerol (50 mM) or glycerol (50mM) plus propionate (10 mM) served as the carbon and electron sources, respectively. Potassium nitrate (50 mM) was the electron acceptor under anoxic conditions. PGCGROWTHCONDITIONS
Cluster detection and base calling were performed using RTA v1.13 (Illumina), and the quality of the reads was assessed with CASAVA v1.8.1 (Illumina). PGCGROWTHCONDITIONS
delta-rnr mutant_oxic_glycerol PGCGROWTHCONDITIONS
d_rnr O2 1 PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Gene expression was calculated as reads per gene by determining the number of reads that overlapped with the annotated gene loci using HTSeq (Anders et al., 2015, doi: 10.1093/bioinformatics/btu638) with the option 'intersection-nonempty'. PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 E. coli K12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: K-12 delta-rnr mutant (JW5741-1) PGCGROWTHCONDITIONS
molecule subtype: total RNA (ribosome-depleted) PGCGROWTHCONDITIONS
No further treatment was applied. PGCGROWTHCONDITIONS
oxic/anoxic: oxic PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Strand-specific cDNA libraries were prepared from 50 ng of rRNA-depleted samples following the TruSeq RNA protocol (Illumina, San Diego, CA, USA, without purification) with modification of the 2nd strand cDNA synthesis as previously described (Parkhomchuk et al. 2009). The libraries were prepared using multiplex primers to allow simultaneous sequencing in a single lane. Sequencing was performed on a HiSeq1500 using SBS v3 kits (Illumina) to generate paired-end reads of 2 x 50 nucleotides. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPG (reads per gene) files were created using HTSeq, mapping raw reads (fastq format) against the E. coli K12 genome and using a GFF file derived from the annotation of NC_000913.3 available from NCBI. PGCGROWTHCONDITIONS
The sequence data were mapped against the genome sequence of E. coli K12 substr. MG1655 (NCBI accession number NC_000913.3) using Bowtie2 (Langmead and Salzberg, 2012, doi:10.1038/nmeth.1923). PGCGROWTHCONDITIONS
Total RNA was isolated with the RNeasy Protect Bacteria Mini Kit from Qiagen (Hilden, Germany). The isolated RNA was further purified from genomic DNA contaminations using Ambion DNase I treatment following the manufacturer's instructions (DNA-free, Ambion by Life Technologies, Darmstadt, Germany). RNA samples were further subjected to an mRNA enrichment step using the MICROBExpress Kit from Ambion according to the manufacturer`s instructions (Life Technologies, Darmstadt, Germany). PGCGROWTHCONDITIONS
carbon source: glycerol PGCGROWTHCONDITIONS
Cells were grown at 37°C in M4 minimal medium under oxic and anoxic conditions. The minimal medium (1.27 mM K2HPO4, 0.73 mM KH2PO4, 5 mM sodium HEPES, 150 mM NaCl, 9 mM (NH4)2SO4) was supplemented with 0.1 g/l caseinhydrolysate 1 mM MgSO4, 0.1 mM CaCl2 and trace elements (5 μM CoCl2, 0.2 μM CuSO4, 57 μM H3BO3, 5.4 μM FeCl2, 1.3 μM MnSO4, 67.2 μM Na2EDTA, 3.9 μM Na2MoO4, 1.5 μM Na2SeO4, 5 μM NiCl2, and 1 μM ZnSO4). The pH of the media was adjusted to 7.2. Glycerol (50 mM) or glycerol (50mM) plus propionate (10 mM) served as the carbon and electron sources, respectively. Potassium nitrate (50 mM) was the electron acceptor under anoxic conditions. PGCGROWTHCONDITIONS
Cluster detection and base calling were performed using RTA v1.13 (Illumina), and the quality of the reads was assessed with CASAVA v1.8.1 (Illumina). PGCGROWTHCONDITIONS
delta-rnr mutant_oxic_glycerol PGCGROWTHCONDITIONS
d_rnr O2 2 PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Gene expression was calculated as reads per gene by determining the number of reads that overlapped with the annotated gene loci using HTSeq (Anders et al., 2015, doi: 10.1093/bioinformatics/btu638) with the option 'intersection-nonempty'. PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 E. coli K12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: K-12 delta-rnr mutant (JW5741-1) PGCGROWTHCONDITIONS
molecule subtype: total RNA (ribosome-depleted) PGCGROWTHCONDITIONS
No further treatment was applied. PGCGROWTHCONDITIONS
oxic/anoxic: oxic PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Strand-specific cDNA libraries were prepared from 50 ng of rRNA-depleted samples following the TruSeq RNA protocol (Illumina, San Diego, CA, USA, without purification) with modification of the 2nd strand cDNA synthesis as previously described (Parkhomchuk et al. 2009). The libraries were prepared using multiplex primers to allow simultaneous sequencing in a single lane. Sequencing was performed on a HiSeq1500 using SBS v3 kits (Illumina) to generate paired-end reads of 2 x 50 nucleotides. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPG (reads per gene) files were created using HTSeq, mapping raw reads (fastq format) against the E. coli K12 genome and using a GFF file derived from the annotation of NC_000913.3 available from NCBI. PGCGROWTHCONDITIONS
The sequence data were mapped against the genome sequence of E. coli K12 substr. MG1655 (NCBI accession number NC_000913.3) using Bowtie2 (Langmead and Salzberg, 2012, doi:10.1038/nmeth.1923). PGCGROWTHCONDITIONS
Total RNA was isolated with the RNeasy Protect Bacteria Mini Kit from Qiagen (Hilden, Germany). The isolated RNA was further purified from genomic DNA contaminations using Ambion DNase I treatment following the manufacturer's instructions (DNA-free, Ambion by Life Technologies, Darmstadt, Germany). RNA samples were further subjected to an mRNA enrichment step using the MICROBExpress Kit from Ambion according to the manufacturer`s instructions (Life Technologies, Darmstadt, Germany). PGCGROWTHCONDITIONS
carbon source: glycerol + propionate PGCGROWTHCONDITIONS
Cells were grown at 37°C in M4 minimal medium under oxic and anoxic conditions. The minimal medium (1.27 mM K2HPO4, 0.73 mM KH2PO4, 5 mM sodium HEPES, 150 mM NaCl, 9 mM (NH4)2SO4) was supplemented with 0.1 g/l caseinhydrolysate 1 mM MgSO4, 0.1 mM CaCl2 and trace elements (5 μM CoCl2, 0.2 μM CuSO4, 57 μM H3BO3, 5.4 μM FeCl2, 1.3 μM MnSO4, 67.2 μM Na2EDTA, 3.9 μM Na2MoO4, 1.5 μM Na2SeO4, 5 μM NiCl2, and 1 μM ZnSO4). The pH of the media was adjusted to 7.2. Glycerol (50 mM) or glycerol (50mM) plus propionate (10 mM) served as the carbon and electron sources, respectively. Potassium nitrate (50 mM) was the electron acceptor under anoxic conditions. PGCGROWTHCONDITIONS
Cluster detection and base calling were performed using RTA v1.13 (Illumina), and the quality of the reads was assessed with CASAVA v1.8.1 (Illumina). PGCGROWTHCONDITIONS
delta-rnr mutant_anoxic (NO3)_glycerol + propionate PGCGROWTHCONDITIONS
d_rnr NO3 w/propionate 1 PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Gene expression was calculated as reads per gene by determining the number of reads that overlapped with the annotated gene loci using HTSeq (Anders et al., 2015, doi: 10.1093/bioinformatics/btu638) with the option 'intersection-nonempty'. PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 E. coli K12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: K-12 delta-rnr mutant (JW5741-1) PGCGROWTHCONDITIONS
molecule subtype: total RNA (ribosome-depleted) PGCGROWTHCONDITIONS
No further treatment was applied. PGCGROWTHCONDITIONS
oxic/anoxic: anoxic (NO3) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Strand-specific cDNA libraries were prepared from 50 ng of rRNA-depleted samples following the TruSeq RNA protocol (Illumina, San Diego, CA, USA, without purification) with modification of the 2nd strand cDNA synthesis as previously described (Parkhomchuk et al. 2009). The libraries were prepared using multiplex primers to allow simultaneous sequencing in a single lane. Sequencing was performed on a HiSeq1500 using SBS v3 kits (Illumina) to generate paired-end reads of 2 x 50 nucleotides. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPG (reads per gene) files were created using HTSeq, mapping raw reads (fastq format) against the E. coli K12 genome and using a GFF file derived from the annotation of NC_000913.3 available from NCBI. PGCGROWTHCONDITIONS
The sequence data were mapped against the genome sequence of E. coli K12 substr. MG1655 (NCBI accession number NC_000913.3) using Bowtie2 (Langmead and Salzberg, 2012, doi:10.1038/nmeth.1923). PGCGROWTHCONDITIONS
Total RNA was isolated with the RNeasy Protect Bacteria Mini Kit from Qiagen (Hilden, Germany). The isolated RNA was further purified from genomic DNA contaminations using Ambion DNase I treatment following the manufacturer's instructions (DNA-free, Ambion by Life Technologies, Darmstadt, Germany). RNA samples were further subjected to an mRNA enrichment step using the MICROBExpress Kit from Ambion according to the manufacturer`s instructions (Life Technologies, Darmstadt, Germany). PGCGROWTHCONDITIONS
carbon source: glycerol + propionate PGCGROWTHCONDITIONS
Cells were grown at 37°C in M4 minimal medium under oxic and anoxic conditions. The minimal medium (1.27 mM K2HPO4, 0.73 mM KH2PO4, 5 mM sodium HEPES, 150 mM NaCl, 9 mM (NH4)2SO4) was supplemented with 0.1 g/l caseinhydrolysate 1 mM MgSO4, 0.1 mM CaCl2 and trace elements (5 μM CoCl2, 0.2 μM CuSO4, 57 μM H3BO3, 5.4 μM FeCl2, 1.3 μM MnSO4, 67.2 μM Na2EDTA, 3.9 μM Na2MoO4, 1.5 μM Na2SeO4, 5 μM NiCl2, and 1 μM ZnSO4). The pH of the media was adjusted to 7.2. Glycerol (50 mM) or glycerol (50mM) plus propionate (10 mM) served as the carbon and electron sources, respectively. Potassium nitrate (50 mM) was the electron acceptor under anoxic conditions. PGCGROWTHCONDITIONS
Cluster detection and base calling were performed using RTA v1.13 (Illumina), and the quality of the reads was assessed with CASAVA v1.8.1 (Illumina). PGCGROWTHCONDITIONS
delta-rnr mutant_anoxic (NO3)_glycerol + propionate PGCGROWTHCONDITIONS
d_rnr NO3 w/propionate 2 PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Gene expression was calculated as reads per gene by determining the number of reads that overlapped with the annotated gene loci using HTSeq (Anders et al., 2015, doi: 10.1093/bioinformatics/btu638) with the option 'intersection-nonempty'. PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 E. coli K12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: K-12 delta-rnr mutant (JW5741-1) PGCGROWTHCONDITIONS
molecule subtype: total RNA (ribosome-depleted) PGCGROWTHCONDITIONS
No further treatment was applied. PGCGROWTHCONDITIONS
oxic/anoxic: anoxic (NO3) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Strand-specific cDNA libraries were prepared from 50 ng of rRNA-depleted samples following the TruSeq RNA protocol (Illumina, San Diego, CA, USA, without purification) with modification of the 2nd strand cDNA synthesis as previously described (Parkhomchuk et al. 2009). The libraries were prepared using multiplex primers to allow simultaneous sequencing in a single lane. Sequencing was performed on a HiSeq1500 using SBS v3 kits (Illumina) to generate paired-end reads of 2 x 50 nucleotides. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPG (reads per gene) files were created using HTSeq, mapping raw reads (fastq format) against the E. coli K12 genome and using a GFF file derived from the annotation of NC_000913.3 available from NCBI. PGCGROWTHCONDITIONS
The sequence data were mapped against the genome sequence of E. coli K12 substr. MG1655 (NCBI accession number NC_000913.3) using Bowtie2 (Langmead and Salzberg, 2012, doi:10.1038/nmeth.1923). PGCGROWTHCONDITIONS
Total RNA was isolated with the RNeasy Protect Bacteria Mini Kit from Qiagen (Hilden, Germany). The isolated RNA was further purified from genomic DNA contaminations using Ambion DNase I treatment following the manufacturer's instructions (DNA-free, Ambion by Life Technologies, Darmstadt, Germany). RNA samples were further subjected to an mRNA enrichment step using the MICROBExpress Kit from Ambion according to the manufacturer`s instructions (Life Technologies, Darmstadt, Germany). PGCGROWTHCONDITIONS
carbon source: glycerol + propionate PGCGROWTHCONDITIONS
Cells were grown at 37°C in M4 minimal medium under oxic and anoxic conditions. The minimal medium (1.27 mM K2HPO4, 0.73 mM KH2PO4, 5 mM sodium HEPES, 150 mM NaCl, 9 mM (NH4)2SO4) was supplemented with 0.1 g/l caseinhydrolysate 1 mM MgSO4, 0.1 mM CaCl2 and trace elements (5 μM CoCl2, 0.2 μM CuSO4, 57 μM H3BO3, 5.4 μM FeCl2, 1.3 μM MnSO4, 67.2 μM Na2EDTA, 3.9 μM Na2MoO4, 1.5 μM Na2SeO4, 5 μM NiCl2, and 1 μM ZnSO4). The pH of the media was adjusted to 7.2. Glycerol (50 mM) or glycerol (50mM) plus propionate (10 mM) served as the carbon and electron sources, respectively. Potassium nitrate (50 mM) was the electron acceptor under anoxic conditions. PGCGROWTHCONDITIONS
Cluster detection and base calling were performed using RTA v1.13 (Illumina), and the quality of the reads was assessed with CASAVA v1.8.1 (Illumina). PGCGROWTHCONDITIONS
delta-rnr mutant_oxic_glycerol + propionate PGCGROWTHCONDITIONS
d_rnr O2 w/propionate 1 PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Gene expression was calculated as reads per gene by determining the number of reads that overlapped with the annotated gene loci using HTSeq (Anders et al., 2015, doi: 10.1093/bioinformatics/btu638) with the option 'intersection-nonempty'. PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 E. coli K12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: K-12 delta-rnr mutant (JW5741-1) PGCGROWTHCONDITIONS
molecule subtype: total RNA (ribosome-depleted) PGCGROWTHCONDITIONS
No further treatment was applied. PGCGROWTHCONDITIONS
oxic/anoxic: oxic PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Strand-specific cDNA libraries were prepared from 50 ng of rRNA-depleted samples following the TruSeq RNA protocol (Illumina, San Diego, CA, USA, without purification) with modification of the 2nd strand cDNA synthesis as previously described (Parkhomchuk et al. 2009). The libraries were prepared using multiplex primers to allow simultaneous sequencing in a single lane. Sequencing was performed on a HiSeq1500 using SBS v3 kits (Illumina) to generate paired-end reads of 2 x 50 nucleotides. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPG (reads per gene) files were created using HTSeq, mapping raw reads (fastq format) against the E. coli K12 genome and using a GFF file derived from the annotation of NC_000913.3 available from NCBI. PGCGROWTHCONDITIONS
The sequence data were mapped against the genome sequence of E. coli K12 substr. MG1655 (NCBI accession number NC_000913.3) using Bowtie2 (Langmead and Salzberg, 2012, doi:10.1038/nmeth.1923). PGCGROWTHCONDITIONS
Total RNA was isolated with the RNeasy Protect Bacteria Mini Kit from Qiagen (Hilden, Germany). The isolated RNA was further purified from genomic DNA contaminations using Ambion DNase I treatment following the manufacturer's instructions (DNA-free, Ambion by Life Technologies, Darmstadt, Germany). RNA samples were further subjected to an mRNA enrichment step using the MICROBExpress Kit from Ambion according to the manufacturer`s instructions (Life Technologies, Darmstadt, Germany). PGCGROWTHCONDITIONS
carbon source: glycerol + propionate PGCGROWTHCONDITIONS
Cells were grown at 37°C in M4 minimal medium under oxic and anoxic conditions. The minimal medium (1.27 mM K2HPO4, 0.73 mM KH2PO4, 5 mM sodium HEPES, 150 mM NaCl, 9 mM (NH4)2SO4) was supplemented with 0.1 g/l caseinhydrolysate 1 mM MgSO4, 0.1 mM CaCl2 and trace elements (5 μM CoCl2, 0.2 μM CuSO4, 57 μM H3BO3, 5.4 μM FeCl2, 1.3 μM MnSO4, 67.2 μM Na2EDTA, 3.9 μM Na2MoO4, 1.5 μM Na2SeO4, 5 μM NiCl2, and 1 μM ZnSO4). The pH of the media was adjusted to 7.2. Glycerol (50 mM) or glycerol (50mM) plus propionate (10 mM) served as the carbon and electron sources, respectively. Potassium nitrate (50 mM) was the electron acceptor under anoxic conditions. PGCGROWTHCONDITIONS
Cluster detection and base calling were performed using RTA v1.13 (Illumina), and the quality of the reads was assessed with CASAVA v1.8.1 (Illumina). PGCGROWTHCONDITIONS
delta-rnr mutant_oxic_glycerol + propionate PGCGROWTHCONDITIONS
d_rnr O2 w/propionate 2 PGCGROWTHCONDITIONS
Escherichia coli K-12 PGCGROWTHCONDITIONS
Gene expression was calculated as reads per gene by determining the number of reads that overlapped with the annotated gene loci using HTSeq (Anders et al., 2015, doi: 10.1093/bioinformatics/btu638) with the option 'intersection-nonempty'. PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 E. coli K12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: K-12 delta-rnr mutant (JW5741-1) PGCGROWTHCONDITIONS
molecule subtype: total RNA (ribosome-depleted) PGCGROWTHCONDITIONS
No further treatment was applied. PGCGROWTHCONDITIONS
oxic/anoxic: oxic PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Strand-specific cDNA libraries were prepared from 50 ng of rRNA-depleted samples following the TruSeq RNA protocol (Illumina, San Diego, CA, USA, without purification) with modification of the 2nd strand cDNA synthesis as previously described (Parkhomchuk et al. 2009). The libraries were prepared using multiplex primers to allow simultaneous sequencing in a single lane. Sequencing was performed on a HiSeq1500 using SBS v3 kits (Illumina) to generate paired-end reads of 2 x 50 nucleotides. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: RPG (reads per gene) files were created using HTSeq, mapping raw reads (fastq format) against the E. coli K12 genome and using a GFF file derived from the annotation of NC_000913.3 available from NCBI. PGCGROWTHCONDITIONS
The sequence data were mapped against the genome sequence of E. coli K12 substr. MG1655 (NCBI accession number NC_000913.3) using Bowtie2 (Langmead and Salzberg, 2012, doi:10.1038/nmeth.1923). PGCGROWTHCONDITIONS
Total RNA was isolated with the RNeasy Protect Bacteria Mini Kit from Qiagen (Hilden, Germany). The isolated RNA was further purified from genomic DNA contaminations using Ambion DNase I treatment following the manufacturer's instructions (DNA-free, Ambion by Life Technologies, Darmstadt, Germany). RNA samples were further subjected to an mRNA enrichment step using the MICROBExpress Kit from Ambion according to the manufacturer`s instructions (Life Technologies, Darmstadt, Germany). PGCGROWTHCONDITIONS
Alignment to the E. coli K12 MG1655 genome sequence was performed using TMAP map4 algorithm with 5' and 3' soft-clipping and a minimum seed length of 20 nt PGCGROWTHCONDITIONS
Basecalling was performed by Torrent Suite version 5 software using the default settings. PGCGROWTHCONDITIONS
Briefly, hot phenol-chloroform extraction was done by mixing the cell culture in ½ volume of 99°C lysis solution (2% SDS, 16 mM EDTA, 200 mM NaCl made in RNAse-free H2O) for 10 min. The suspension was extracted twice with 1 volume of 65°C acid phenol/chloroform (pH 4.5), once in chloroform/isoamyl alcohol, and precipitated with isopropanol. Pellets were washed with 1 mL of 70% ethanol, dried and purified using QIAGEN RNeasy kit. Final RNA was eluted with 100 µL of nuclease-free water. Following purification, DNAse treatment with TURBO DNase kit was performed according to manufacturer’s manual, except that twice amount of recommended DNase inactivation reagent was used. The integrity of DNA-free RNA was analyzed on either native agarose gel or on Agilent Bioanalyzer RNA 6000 Nano chip. PGCGROWTHCONDITIONS
E. coli strain K12 PGCGROWTHCONDITIONS
E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655, NCBI Reference Sequence: NC_000913.3 PGCGROWTHCONDITIONS
Ion Xpress barcoded libraries were constructed using the Ribo-Zero Magnatic Kit (Gram-negative bacteria, Epicentre )and IonXpress RNA-seq v2 (Life Technologies) kits according to the manufacturer's directions. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Microsoft Excel File with normalized sequencing coverage of all annotated genes and statistical comparison of expression in antibiotic treated to untreated cells . PGCGROWTHCONDITIONS
The cells were untreated, or treated with  (100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70% Ethanol). After 10 minutes at 37°C, 1 mL samples were subjected to hot phenol-chloroform extraction. Ref: Chuang SE, Daniels DL, and Blattner FR (1993) Global regulation of gene expression in Escherichia coli. J. Bacteriol. 175:2026-2036. PGCGROWTHCONDITIONS
The total sequencing base pair coverage for all annotated genes was summed for each sample and normalized to total coverage using bedtools and custom R scripts as described in Wu et al. 2015 PLoS Genetics Nov 6;11(11):e1005655. PGCGROWTHCONDITIONS
treatment: untreated PGCGROWTHCONDITIONS
Untreated_replicate_1 PGCGROWTHCONDITIONS
Alignment to the E. coli K12 MG1655 genome sequence was performed using TMAP map4 algorithm with 5' and 3' soft-clipping and a minimum seed length of 20 nt PGCGROWTHCONDITIONS
Basecalling was performed by Torrent Suite version 5 software using the default settings. PGCGROWTHCONDITIONS
Briefly, hot phenol-chloroform extraction was done by mixing the cell culture in ½ volume of 99°C lysis solution (2% SDS, 16 mM EDTA, 200 mM NaCl made in RNAse-free H2O) for 10 min. The suspension was extracted twice with 1 volume of 65°C acid phenol/chloroform (pH 4.5), once in chloroform/isoamyl alcohol, and precipitated with isopropanol. Pellets were washed with 1 mL of 70% ethanol, dried and purified using QIAGEN RNeasy kit. Final RNA was eluted with 100 µL of nuclease-free water. Following purification, DNAse treatment with TURBO DNase kit was performed according to manufacturer’s manual, except that twice amount of recommended DNase inactivation reagent was used. The integrity of DNA-free RNA was analyzed on either native agarose gel or on Agilent Bioanalyzer RNA 6000 Nano chip. PGCGROWTHCONDITIONS
E. coli strain K12 PGCGROWTHCONDITIONS
E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655, NCBI Reference Sequence: NC_000913.3 PGCGROWTHCONDITIONS
Ion Xpress barcoded libraries were constructed using the Ribo-Zero Magnatic Kit (Gram-negative bacteria, Epicentre )and IonXpress RNA-seq v2 (Life Technologies) kits according to the manufacturer's directions. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Microsoft Excel File with normalized sequencing coverage of all annotated genes and statistical comparison of expression in antibiotic treated to untreated cells . PGCGROWTHCONDITIONS
The cells were untreated, or treated with  (100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70% Ethanol). After 10 minutes at 37°C, 1 mL samples were subjected to hot phenol-chloroform extraction. Ref: Chuang SE, Daniels DL, and Blattner FR (1993) Global regulation of gene expression in Escherichia coli. J. Bacteriol. 175:2026-2036. PGCGROWTHCONDITIONS
The total sequencing base pair coverage for all annotated genes was summed for each sample and normalized to total coverage using bedtools and custom R scripts as described in Wu et al. 2015 PLoS Genetics Nov 6;11(11):e1005655. PGCGROWTHCONDITIONS
treatment: untreated PGCGROWTHCONDITIONS
Untreated_replicate_2 PGCGROWTHCONDITIONS
Alignment to the E. coli K12 MG1655 genome sequence was performed using TMAP map4 algorithm with 5' and 3' soft-clipping and a minimum seed length of 20 nt PGCGROWTHCONDITIONS
Basecalling was performed by Torrent Suite version 5 software using the default settings. PGCGROWTHCONDITIONS
Briefly, hot phenol-chloroform extraction was done by mixing the cell culture in ½ volume of 99°C lysis solution (2% SDS, 16 mM EDTA, 200 mM NaCl made in RNAse-free H2O) for 10 min. The suspension was extracted twice with 1 volume of 65°C acid phenol/chloroform (pH 4.5), once in chloroform/isoamyl alcohol, and precipitated with isopropanol. Pellets were washed with 1 mL of 70% ethanol, dried and purified using QIAGEN RNeasy kit. Final RNA was eluted with 100 µL of nuclease-free water. Following purification, DNAse treatment with TURBO DNase kit was performed according to manufacturer’s manual, except that twice amount of recommended DNase inactivation reagent was used. The integrity of DNA-free RNA was analyzed on either native agarose gel or on Agilent Bioanalyzer RNA 6000 Nano chip. PGCGROWTHCONDITIONS
E. coli strain K12 PGCGROWTHCONDITIONS
E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655, NCBI Reference Sequence: NC_000913.3 PGCGROWTHCONDITIONS
Ion Xpress barcoded libraries were constructed using the Ribo-Zero Magnatic Kit (Gram-negative bacteria, Epicentre )and IonXpress RNA-seq v2 (Life Technologies) kits according to the manufacturer's directions. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Microsoft Excel File with normalized sequencing coverage of all annotated genes and statistical comparison of expression in antibiotic treated to untreated cells . PGCGROWTHCONDITIONS
The cells were untreated, or treated with  (100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70% Ethanol). After 10 minutes at 37°C, 1 mL samples were subjected to hot phenol-chloroform extraction. Ref: Chuang SE, Daniels DL, and Blattner FR (1993) Global regulation of gene expression in Escherichia coli. J. Bacteriol. 175:2026-2036. PGCGROWTHCONDITIONS
The total sequencing base pair coverage for all annotated genes was summed for each sample and normalized to total coverage using bedtools and custom R scripts as described in Wu et al. 2015 PLoS Genetics Nov 6;11(11):e1005655. PGCGROWTHCONDITIONS
treatment: untreated PGCGROWTHCONDITIONS
Untreated_replicate_3 PGCGROWTHCONDITIONS
Alignment to the E. coli K12 MG1655 genome sequence was performed using TMAP map4 algorithm with 5' and 3' soft-clipping and a minimum seed length of 20 nt PGCGROWTHCONDITIONS
Basecalling was performed by Torrent Suite version 5 software using the default settings. PGCGROWTHCONDITIONS
Briefly, hot phenol-chloroform extraction was done by mixing the cell culture in ½ volume of 99°C lysis solution (2% SDS, 16 mM EDTA, 200 mM NaCl made in RNAse-free H2O) for 10 min. The suspension was extracted twice with 1 volume of 65°C acid phenol/chloroform (pH 4.5), once in chloroform/isoamyl alcohol, and precipitated with isopropanol. Pellets were washed with 1 mL of 70% ethanol, dried and purified using QIAGEN RNeasy kit. Final RNA was eluted with 100 µL of nuclease-free water. Following purification, DNAse treatment with TURBO DNase kit was performed according to manufacturer’s manual, except that twice amount of recommended DNase inactivation reagent was used. The integrity of DNA-free RNA was analyzed on either native agarose gel or on Agilent Bioanalyzer RNA 6000 Nano chip. PGCGROWTHCONDITIONS
E. coli strain K12 PGCGROWTHCONDITIONS
E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS
Erythromycin_replicate_1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655, NCBI Reference Sequence: NC_000913.3 PGCGROWTHCONDITIONS
Ion Xpress barcoded libraries were constructed using the Ribo-Zero Magnatic Kit (Gram-negative bacteria, Epicentre )and IonXpress RNA-seq v2 (Life Technologies) kits according to the manufacturer's directions. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Microsoft Excel File with normalized sequencing coverage of all annotated genes and statistical comparison of expression in antibiotic treated to untreated cells . PGCGROWTHCONDITIONS
The cells were untreated, or treated with  (100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70% Ethanol). After 10 minutes at 37°C, 1 mL samples were subjected to hot phenol-chloroform extraction. Ref: Chuang SE, Daniels DL, and Blattner FR (1993) Global regulation of gene expression in Escherichia coli. J. Bacteriol. 175:2026-2036. PGCGROWTHCONDITIONS
The total sequencing base pair coverage for all annotated genes was summed for each sample and normalized to total coverage using bedtools and custom R scripts as described in Wu et al. 2015 PLoS Genetics Nov 6;11(11):e1005655. PGCGROWTHCONDITIONS
treatment: erythromycin PGCGROWTHCONDITIONS
Alignment to the E. coli K12 MG1655 genome sequence was performed using TMAP map4 algorithm with 5' and 3' soft-clipping and a minimum seed length of 20 nt PGCGROWTHCONDITIONS
Basecalling was performed by Torrent Suite version 5 software using the default settings. PGCGROWTHCONDITIONS
Briefly, hot phenol-chloroform extraction was done by mixing the cell culture in ½ volume of 99°C lysis solution (2% SDS, 16 mM EDTA, 200 mM NaCl made in RNAse-free H2O) for 10 min. The suspension was extracted twice with 1 volume of 65°C acid phenol/chloroform (pH 4.5), once in chloroform/isoamyl alcohol, and precipitated with isopropanol. Pellets were washed with 1 mL of 70% ethanol, dried and purified using QIAGEN RNeasy kit. Final RNA was eluted with 100 µL of nuclease-free water. Following purification, DNAse treatment with TURBO DNase kit was performed according to manufacturer’s manual, except that twice amount of recommended DNase inactivation reagent was used. The integrity of DNA-free RNA was analyzed on either native agarose gel or on Agilent Bioanalyzer RNA 6000 Nano chip. PGCGROWTHCONDITIONS
E. coli strain K12 PGCGROWTHCONDITIONS
E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS
Erythromycin_replicate_2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655, NCBI Reference Sequence: NC_000913.3 PGCGROWTHCONDITIONS
Ion Xpress barcoded libraries were constructed using the Ribo-Zero Magnatic Kit (Gram-negative bacteria, Epicentre )and IonXpress RNA-seq v2 (Life Technologies) kits according to the manufacturer's directions. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Microsoft Excel File with normalized sequencing coverage of all annotated genes and statistical comparison of expression in antibiotic treated to untreated cells . PGCGROWTHCONDITIONS
The cells were untreated, or treated with  (100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70% Ethanol). After 10 minutes at 37°C, 1 mL samples were subjected to hot phenol-chloroform extraction. Ref: Chuang SE, Daniels DL, and Blattner FR (1993) Global regulation of gene expression in Escherichia coli. J. Bacteriol. 175:2026-2036. PGCGROWTHCONDITIONS
The total sequencing base pair coverage for all annotated genes was summed for each sample and normalized to total coverage using bedtools and custom R scripts as described in Wu et al. 2015 PLoS Genetics Nov 6;11(11):e1005655. PGCGROWTHCONDITIONS
treatment: erythromycin PGCGROWTHCONDITIONS
Alignment to the E. coli K12 MG1655 genome sequence was performed using TMAP map4 algorithm with 5' and 3' soft-clipping and a minimum seed length of 20 nt PGCGROWTHCONDITIONS
Basecalling was performed by Torrent Suite version 5 software using the default settings. PGCGROWTHCONDITIONS
Briefly, hot phenol-chloroform extraction was done by mixing the cell culture in ½ volume of 99°C lysis solution (2% SDS, 16 mM EDTA, 200 mM NaCl made in RNAse-free H2O) for 10 min. The suspension was extracted twice with 1 volume of 65°C acid phenol/chloroform (pH 4.5), once in chloroform/isoamyl alcohol, and precipitated with isopropanol. Pellets were washed with 1 mL of 70% ethanol, dried and purified using QIAGEN RNeasy kit. Final RNA was eluted with 100 µL of nuclease-free water. Following purification, DNAse treatment with TURBO DNase kit was performed according to manufacturer’s manual, except that twice amount of recommended DNase inactivation reagent was used. The integrity of DNA-free RNA was analyzed on either native agarose gel or on Agilent Bioanalyzer RNA 6000 Nano chip. PGCGROWTHCONDITIONS
E. coli strain K12 PGCGROWTHCONDITIONS
E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS
Erythromycin_replicate_3 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655, NCBI Reference Sequence: NC_000913.3 PGCGROWTHCONDITIONS
Ion Xpress barcoded libraries were constructed using the Ribo-Zero Magnatic Kit (Gram-negative bacteria, Epicentre )and IonXpress RNA-seq v2 (Life Technologies) kits according to the manufacturer's directions. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Microsoft Excel File with normalized sequencing coverage of all annotated genes and statistical comparison of expression in antibiotic treated to untreated cells . PGCGROWTHCONDITIONS
The cells were untreated, or treated with  (100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70% Ethanol). After 10 minutes at 37°C, 1 mL samples were subjected to hot phenol-chloroform extraction. Ref: Chuang SE, Daniels DL, and Blattner FR (1993) Global regulation of gene expression in Escherichia coli. J. Bacteriol. 175:2026-2036. PGCGROWTHCONDITIONS
The total sequencing base pair coverage for all annotated genes was summed for each sample and normalized to total coverage using bedtools and custom R scripts as described in Wu et al. 2015 PLoS Genetics Nov 6;11(11):e1005655. PGCGROWTHCONDITIONS
treatment: erythromycin PGCGROWTHCONDITIONS
Alignment to the E. coli K12 MG1655 genome sequence was performed using TMAP map4 algorithm with 5' and 3' soft-clipping and a minimum seed length of 20 nt PGCGROWTHCONDITIONS
Basecalling was performed by Torrent Suite version 5 software using the default settings. PGCGROWTHCONDITIONS
Briefly, hot phenol-chloroform extraction was done by mixing the cell culture in ½ volume of 99°C lysis solution (2% SDS, 16 mM EDTA, 200 mM NaCl made in RNAse-free H2O) for 10 min. The suspension was extracted twice with 1 volume of 65°C acid phenol/chloroform (pH 4.5), once in chloroform/isoamyl alcohol, and precipitated with isopropanol. Pellets were washed with 1 mL of 70% ethanol, dried and purified using QIAGEN RNeasy kit. Final RNA was eluted with 100 µL of nuclease-free water. Following purification, DNAse treatment with TURBO DNase kit was performed according to manufacturer’s manual, except that twice amount of recommended DNase inactivation reagent was used. The integrity of DNA-free RNA was analyzed on either native agarose gel or on Agilent Bioanalyzer RNA 6000 Nano chip. PGCGROWTHCONDITIONS
Clindamycin_replicate_1 PGCGROWTHCONDITIONS
E. coli strain K12 PGCGROWTHCONDITIONS
E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655, NCBI Reference Sequence: NC_000913.3 PGCGROWTHCONDITIONS
Ion Xpress barcoded libraries were constructed using the Ribo-Zero Magnatic Kit (Gram-negative bacteria, Epicentre )and IonXpress RNA-seq v2 (Life Technologies) kits according to the manufacturer's directions. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Microsoft Excel File with normalized sequencing coverage of all annotated genes and statistical comparison of expression in antibiotic treated to untreated cells . PGCGROWTHCONDITIONS
The cells were untreated, or treated with  (100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70% Ethanol). After 10 minutes at 37°C, 1 mL samples were subjected to hot phenol-chloroform extraction. Ref: Chuang SE, Daniels DL, and Blattner FR (1993) Global regulation of gene expression in Escherichia coli. J. Bacteriol. 175:2026-2036. PGCGROWTHCONDITIONS
The total sequencing base pair coverage for all annotated genes was summed for each sample and normalized to total coverage using bedtools and custom R scripts as described in Wu et al. 2015 PLoS Genetics Nov 6;11(11):e1005655. PGCGROWTHCONDITIONS
treatment: clindamycin PGCGROWTHCONDITIONS
Alignment to the E. coli K12 MG1655 genome sequence was performed using TMAP map4 algorithm with 5' and 3' soft-clipping and a minimum seed length of 20 nt PGCGROWTHCONDITIONS
Basecalling was performed by Torrent Suite version 5 software using the default settings. PGCGROWTHCONDITIONS
Briefly, hot phenol-chloroform extraction was done by mixing the cell culture in ½ volume of 99°C lysis solution (2% SDS, 16 mM EDTA, 200 mM NaCl made in RNAse-free H2O) for 10 min. The suspension was extracted twice with 1 volume of 65°C acid phenol/chloroform (pH 4.5), once in chloroform/isoamyl alcohol, and precipitated with isopropanol. Pellets were washed with 1 mL of 70% ethanol, dried and purified using QIAGEN RNeasy kit. Final RNA was eluted with 100 µL of nuclease-free water. Following purification, DNAse treatment with TURBO DNase kit was performed according to manufacturer’s manual, except that twice amount of recommended DNase inactivation reagent was used. The integrity of DNA-free RNA was analyzed on either native agarose gel or on Agilent Bioanalyzer RNA 6000 Nano chip. PGCGROWTHCONDITIONS
Clindamycin_replicate_2 PGCGROWTHCONDITIONS
E. coli strain K12 PGCGROWTHCONDITIONS
E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655, NCBI Reference Sequence: NC_000913.3 PGCGROWTHCONDITIONS
Ion Xpress barcoded libraries were constructed using the Ribo-Zero Magnatic Kit (Gram-negative bacteria, Epicentre )and IonXpress RNA-seq v2 (Life Technologies) kits according to the manufacturer's directions. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Microsoft Excel File with normalized sequencing coverage of all annotated genes and statistical comparison of expression in antibiotic treated to untreated cells . PGCGROWTHCONDITIONS
The cells were untreated, or treated with  (100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70% Ethanol). After 10 minutes at 37°C, 1 mL samples were subjected to hot phenol-chloroform extraction. Ref: Chuang SE, Daniels DL, and Blattner FR (1993) Global regulation of gene expression in Escherichia coli. J. Bacteriol. 175:2026-2036. PGCGROWTHCONDITIONS
The total sequencing base pair coverage for all annotated genes was summed for each sample and normalized to total coverage using bedtools and custom R scripts as described in Wu et al. 2015 PLoS Genetics Nov 6;11(11):e1005655. PGCGROWTHCONDITIONS
treatment: clindamycin PGCGROWTHCONDITIONS
Alignment to the E. coli K12 MG1655 genome sequence was performed using TMAP map4 algorithm with 5' and 3' soft-clipping and a minimum seed length of 20 nt PGCGROWTHCONDITIONS
Basecalling was performed by Torrent Suite version 5 software using the default settings. PGCGROWTHCONDITIONS
Briefly, hot phenol-chloroform extraction was done by mixing the cell culture in ½ volume of 99°C lysis solution (2% SDS, 16 mM EDTA, 200 mM NaCl made in RNAse-free H2O) for 10 min. The suspension was extracted twice with 1 volume of 65°C acid phenol/chloroform (pH 4.5), once in chloroform/isoamyl alcohol, and precipitated with isopropanol. Pellets were washed with 1 mL of 70% ethanol, dried and purified using QIAGEN RNeasy kit. Final RNA was eluted with 100 µL of nuclease-free water. Following purification, DNAse treatment with TURBO DNase kit was performed according to manufacturer’s manual, except that twice amount of recommended DNase inactivation reagent was used. The integrity of DNA-free RNA was analyzed on either native agarose gel or on Agilent Bioanalyzer RNA 6000 Nano chip. PGCGROWTHCONDITIONS
Clindamycin_replicate_3 PGCGROWTHCONDITIONS
E. coli strain K12 PGCGROWTHCONDITIONS
E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655, NCBI Reference Sequence: NC_000913.3 PGCGROWTHCONDITIONS
Ion Xpress barcoded libraries were constructed using the Ribo-Zero Magnatic Kit (Gram-negative bacteria, Epicentre )and IonXpress RNA-seq v2 (Life Technologies) kits according to the manufacturer's directions. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Microsoft Excel File with normalized sequencing coverage of all annotated genes and statistical comparison of expression in antibiotic treated to untreated cells . PGCGROWTHCONDITIONS
The cells were untreated, or treated with  (100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70% Ethanol). After 10 minutes at 37°C, 1 mL samples were subjected to hot phenol-chloroform extraction. Ref: Chuang SE, Daniels DL, and Blattner FR (1993) Global regulation of gene expression in Escherichia coli. J. Bacteriol. 175:2026-2036. PGCGROWTHCONDITIONS
The total sequencing base pair coverage for all annotated genes was summed for each sample and normalized to total coverage using bedtools and custom R scripts as described in Wu et al. 2015 PLoS Genetics Nov 6;11(11):e1005655. PGCGROWTHCONDITIONS
treatment: clindamycin PGCGROWTHCONDITIONS
Aerobic 1 PGCGROWTHCONDITIONS
Aerobic and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at 37°C with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture. Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. PGCGROWTHCONDITIONS
Bowtie 2 (Langmead B & Salzberg SL, 2012) was used with default parameters, to remove any sequence reads aligning to ribosomal RNA, transfer RNA and non-coding RNA sequences. PGCGROWTHCONDITIONS
Cultured cells PGCGROWTHCONDITIONS
Differential expression between aerobic and anaerobic environments was identified by using DESeq2 (Love M, Huber W and  Anders S, 2014) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli B str. REL606; NC_012967.1 PGCGROWTHCONDITIONS
growth environment: Aerobic PGCGROWTHCONDITIONS
growth phase: Stationary phase PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-Seq reads were mapped to the reference genome using EDGE-Pro (Magoc T, Wood D and Salzberg SL, 2013) ) with default parameters PGCGROWTHCONDITIONS
RNA was extracted from harvested cultures using a hot lysis buffer and acid phenol-based extraction method and isopropanol precipitation. Following RNA extraction, Turbo DNase (Ambion, USA) was used to treat the samples as per manufacturer’s instructions. Each sample was split into five 20 μL aliquots and two rounds of DNase treatment were performed on each aliquot. Following DNase treatment, RNA samples were purified using the RNeasy Mini kit (Qiagen, Germany) as per the manufacturer’s instructions. For each sample, the DNase-treated aliquots were pooled together before purification. RNA quality was measured using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA) with the RNA 6000 Nano Chip kit according to the manufacturer’s instructions while RNA was quantified using the Quant-iT RNA Assay kit (Life Technologies) and measured on a Qubit® 2.0 fluorometer. RNA was sequenced on the Illumina HiSeq 2000 platform  at BGI (Shenzen, China). PGCGROWTHCONDITIONS
Sequence data from BGI had been filtered to remove reads containing ≥ 10% unreadable bases, ≥ 20% low quality (≤ Q20) bases, adapter contamination or duplicate read-pairs PGCGROWTHCONDITIONS
strain: REL4536 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample PGCGROWTHCONDITIONS
The quality of reads was assessed by using FastQC (Andrews S, 2010) and any reads with a quality score ≤  Q28 were trimmed using Trim Galore! (Krueger F, 2013 ). PGCGROWTHCONDITIONS
Aerobic 2 PGCGROWTHCONDITIONS
Aerobic and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at 37°C with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture. Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. PGCGROWTHCONDITIONS
Bowtie 2 (Langmead B & Salzberg SL, 2012) was used with default parameters, to remove any sequence reads aligning to ribosomal RNA, transfer RNA and non-coding RNA sequences. PGCGROWTHCONDITIONS
Cultured cells PGCGROWTHCONDITIONS
Differential expression between aerobic and anaerobic environments was identified by using DESeq2 (Love M, Huber W and  Anders S, 2014) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli B str. REL606; NC_012967.1 PGCGROWTHCONDITIONS
growth environment: Aerobic PGCGROWTHCONDITIONS
growth phase: Stationary phase PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-Seq reads were mapped to the reference genome using EDGE-Pro (Magoc T, Wood D and Salzberg SL, 2013) ) with default parameters PGCGROWTHCONDITIONS
RNA was extracted from harvested cultures using a hot lysis buffer and acid phenol-based extraction method and isopropanol precipitation. Following RNA extraction, Turbo DNase (Ambion, USA) was used to treat the samples as per manufacturer’s instructions. Each sample was split into five 20 μL aliquots and two rounds of DNase treatment were performed on each aliquot. Following DNase treatment, RNA samples were purified using the RNeasy Mini kit (Qiagen, Germany) as per the manufacturer’s instructions. For each sample, the DNase-treated aliquots were pooled together before purification. RNA quality was measured using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA) with the RNA 6000 Nano Chip kit according to the manufacturer’s instructions while RNA was quantified using the Quant-iT RNA Assay kit (Life Technologies) and measured on a Qubit® 2.0 fluorometer. RNA was sequenced on the Illumina HiSeq 2000 platform  at BGI (Shenzen, China). PGCGROWTHCONDITIONS
Sequence data from BGI had been filtered to remove reads containing ≥ 10% unreadable bases, ≥ 20% low quality (≤ Q20) bases, adapter contamination or duplicate read-pairs PGCGROWTHCONDITIONS
strain: REL4536 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample PGCGROWTHCONDITIONS
The quality of reads was assessed by using FastQC (Andrews S, 2010) and any reads with a quality score ≤  Q28 were trimmed using Trim Galore! (Krueger F, 2013 ). PGCGROWTHCONDITIONS
Aerobic 3 PGCGROWTHCONDITIONS
Aerobic and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at 37°C with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture. Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. PGCGROWTHCONDITIONS
Bowtie 2 (Langmead B & Salzberg SL, 2012) was used with default parameters, to remove any sequence reads aligning to ribosomal RNA, transfer RNA and non-coding RNA sequences. PGCGROWTHCONDITIONS
Cultured cells PGCGROWTHCONDITIONS
Differential expression between aerobic and anaerobic environments was identified by using DESeq2 (Love M, Huber W and  Anders S, 2014) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli B str. REL606; NC_012967.1 PGCGROWTHCONDITIONS
growth environment: Aerobic PGCGROWTHCONDITIONS
growth phase: Stationary phase PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-Seq reads were mapped to the reference genome using EDGE-Pro (Magoc T, Wood D and Salzberg SL, 2013) ) with default parameters PGCGROWTHCONDITIONS
RNA was extracted from harvested cultures using a hot lysis buffer and acid phenol-based extraction method and isopropanol precipitation. Following RNA extraction, Turbo DNase (Ambion, USA) was used to treat the samples as per manufacturer’s instructions. Each sample was split into five 20 μL aliquots and two rounds of DNase treatment were performed on each aliquot. Following DNase treatment, RNA samples were purified using the RNeasy Mini kit (Qiagen, Germany) as per the manufacturer’s instructions. For each sample, the DNase-treated aliquots were pooled together before purification. RNA quality was measured using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA) with the RNA 6000 Nano Chip kit according to the manufacturer’s instructions while RNA was quantified using the Quant-iT RNA Assay kit (Life Technologies) and measured on a Qubit® 2.0 fluorometer. RNA was sequenced on the Illumina HiSeq 2000 platform  at BGI (Shenzen, China). PGCGROWTHCONDITIONS
Sequence data from BGI had been filtered to remove reads containing ≥ 10% unreadable bases, ≥ 20% low quality (≤ Q20) bases, adapter contamination or duplicate read-pairs PGCGROWTHCONDITIONS
strain: REL4536 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample PGCGROWTHCONDITIONS
The quality of reads was assessed by using FastQC (Andrews S, 2010) and any reads with a quality score ≤  Q28 were trimmed using Trim Galore! (Krueger F, 2013 ). PGCGROWTHCONDITIONS
Aerobic and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at 37°C with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture. Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. PGCGROWTHCONDITIONS
Anaerobic 1 PGCGROWTHCONDITIONS
Bowtie 2 (Langmead B & Salzberg SL, 2012) was used with default parameters, to remove any sequence reads aligning to ribosomal RNA, transfer RNA and non-coding RNA sequences. PGCGROWTHCONDITIONS
Cultured cells PGCGROWTHCONDITIONS
Differential expression between aerobic and anaerobic environments was identified by using DESeq2 (Love M, Huber W and  Anders S, 2014) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli B str. REL606; NC_012967.1 PGCGROWTHCONDITIONS
growth environment: Anaerobic PGCGROWTHCONDITIONS
growth phase: Stationary phase PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-Seq reads were mapped to the reference genome using EDGE-Pro (Magoc T, Wood D and Salzberg SL, 2013) ) with default parameters PGCGROWTHCONDITIONS
RNA was extracted from harvested cultures using a hot lysis buffer and acid phenol-based extraction method and isopropanol precipitation. Following RNA extraction, Turbo DNase (Ambion, USA) was used to treat the samples as per manufacturer’s instructions. Each sample was split into five 20 μL aliquots and two rounds of DNase treatment were performed on each aliquot. Following DNase treatment, RNA samples were purified using the RNeasy Mini kit (Qiagen, Germany) as per the manufacturer’s instructions. For each sample, the DNase-treated aliquots were pooled together before purification. RNA quality was measured using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA) with the RNA 6000 Nano Chip kit according to the manufacturer’s instructions while RNA was quantified using the Quant-iT RNA Assay kit (Life Technologies) and measured on a Qubit® 2.0 fluorometer. RNA was sequenced on the Illumina HiSeq 2000 platform  at BGI (Shenzen, China). PGCGROWTHCONDITIONS
Sequence data from BGI had been filtered to remove reads containing ≥ 10% unreadable bases, ≥ 20% low quality (≤ Q20) bases, adapter contamination or duplicate read-pairs PGCGROWTHCONDITIONS
strain: REL4536 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample PGCGROWTHCONDITIONS
The quality of reads was assessed by using FastQC (Andrews S, 2010) and any reads with a quality score ≤  Q28 were trimmed using Trim Galore! (Krueger F, 2013 ). PGCGROWTHCONDITIONS
Aerobic and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at 37°C with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture. Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. PGCGROWTHCONDITIONS
Anaerobic 3 PGCGROWTHCONDITIONS
Bowtie 2 (Langmead B & Salzberg SL, 2012) was used with default parameters, to remove any sequence reads aligning to ribosomal RNA, transfer RNA and non-coding RNA sequences. PGCGROWTHCONDITIONS
Cultured cells PGCGROWTHCONDITIONS
Differential expression between aerobic and anaerobic environments was identified by using DESeq2 (Love M, Huber W and  Anders S, 2014) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli B str. REL606; NC_012967.1 PGCGROWTHCONDITIONS
growth environment: Anaerobic PGCGROWTHCONDITIONS
growth phase: Stationary phase PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-Seq reads were mapped to the reference genome using EDGE-Pro (Magoc T, Wood D and Salzberg SL, 2013) ) with default parameters PGCGROWTHCONDITIONS
RNA was extracted from harvested cultures using a hot lysis buffer and acid phenol-based extraction method and isopropanol precipitation. Following RNA extraction, Turbo DNase (Ambion, USA) was used to treat the samples as per manufacturer’s instructions. Each sample was split into five 20 μL aliquots and two rounds of DNase treatment were performed on each aliquot. Following DNase treatment, RNA samples were purified using the RNeasy Mini kit (Qiagen, Germany) as per the manufacturer’s instructions. For each sample, the DNase-treated aliquots were pooled together before purification. RNA quality was measured using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA) with the RNA 6000 Nano Chip kit according to the manufacturer’s instructions while RNA was quantified using the Quant-iT RNA Assay kit (Life Technologies) and measured on a Qubit® 2.0 fluorometer. RNA was sequenced on the Illumina HiSeq 2000 platform  at BGI (Shenzen, China). PGCGROWTHCONDITIONS
Sequence data from BGI had been filtered to remove reads containing ≥ 10% unreadable bases, ≥ 20% low quality (≤ Q20) bases, adapter contamination or duplicate read-pairs PGCGROWTHCONDITIONS
strain: REL4536 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample PGCGROWTHCONDITIONS
The quality of reads was assessed by using FastQC (Andrews S, 2010) and any reads with a quality score ≤  Q28 were trimmed using Trim Galore! (Krueger F, 2013 ). PGCGROWTHCONDITIONS
BAM files of the resulting assembly data were exported to JMP Genomics (SAS).  TMM normalization and ANOVA analysis of the read samples were conducted in JMP Genomics PGCGROWTHCONDITIONS
Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C. PGCGROWTHCONDITIONS
Cells were grown to approximately mid-log phase (OD560 = approximately 0.5) in LB. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype: Wildtype PGCGROWTHCONDITIONS
MG1655_1 PGCGROWTHCONDITIONS
MG1655 pCA24N and MG1655 pCA24N-Mfd cells were grown to an OD560 of approximately 0.25 and treated with 100 μM IPTG for 1 hour. PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
Read coverage maps and RPKM data was subsequently generated by Geneious. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads (approximately 13 to 25 million per sample) were imported into Geneious Pro (Biomatters) and assembled to the reference chromosome MG1655 (GenBank Accession Number 000913.2). The assembly process was set to medium/low sensitivity on Geneious, with the following parameters: 10% gaps allowed per read; word length of 18; index word length of 13; words repeated more than 12 times ignored; 20% maximum mismatches per read; and maximum ambiguity of 4 PGCGROWTHCONDITIONS
BAM files of the resulting assembly data were exported to JMP Genomics (SAS).  TMM normalization and ANOVA analysis of the read samples were conducted in JMP Genomics PGCGROWTHCONDITIONS
Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C. PGCGROWTHCONDITIONS
Cells were grown to approximately mid-log phase (OD560 = approximately 0.5) in LB. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype: Wildtype PGCGROWTHCONDITIONS
MG1655_2 PGCGROWTHCONDITIONS
MG1655 pCA24N and MG1655 pCA24N-Mfd cells were grown to an OD560 of approximately 0.25 and treated with 100 μM IPTG for 1 hour. PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
Read coverage maps and RPKM data was subsequently generated by Geneious. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads (approximately 13 to 25 million per sample) were imported into Geneious Pro (Biomatters) and assembled to the reference chromosome MG1655 (GenBank Accession Number 000913.2). The assembly process was set to medium/low sensitivity on Geneious, with the following parameters: 10% gaps allowed per read; word length of 18; index word length of 13; words repeated more than 12 times ignored; 20% maximum mismatches per read; and maximum ambiguity of 4 PGCGROWTHCONDITIONS
BAM files of the resulting assembly data were exported to JMP Genomics (SAS).  TMM normalization and ANOVA analysis of the read samples were conducted in JMP Genomics PGCGROWTHCONDITIONS
Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C. PGCGROWTHCONDITIONS
Cells were grown to approximately mid-log phase (OD560 = approximately 0.5) in LB. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype: Wildtype PGCGROWTHCONDITIONS
MG1655_3 PGCGROWTHCONDITIONS
MG1655 pCA24N and MG1655 pCA24N-Mfd cells were grown to an OD560 of approximately 0.25 and treated with 100 μM IPTG for 1 hour. PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
Read coverage maps and RPKM data was subsequently generated by Geneious. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads (approximately 13 to 25 million per sample) were imported into Geneious Pro (Biomatters) and assembled to the reference chromosome MG1655 (GenBank Accession Number 000913.2). The assembly process was set to medium/low sensitivity on Geneious, with the following parameters: 10% gaps allowed per read; word length of 18; index word length of 13; words repeated more than 12 times ignored; 20% maximum mismatches per read; and maximum ambiguity of 4 PGCGROWTHCONDITIONS
BAM files of the resulting assembly data were exported to JMP Genomics (SAS).  TMM normalization and ANOVA analysis of the read samples were conducted in JMP Genomics PGCGROWTHCONDITIONS
Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C. PGCGROWTHCONDITIONS
Cells were grown to approximately mid-log phase (OD560 = approximately 0.5) in LB. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype: mfd- PGCGROWTHCONDITIONS
mfd_1 PGCGROWTHCONDITIONS
MG1655 pCA24N and MG1655 pCA24N-Mfd cells were grown to an OD560 of approximately 0.25 and treated with 100 μM IPTG for 1 hour. PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
Read coverage maps and RPKM data was subsequently generated by Geneious. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads (approximately 13 to 25 million per sample) were imported into Geneious Pro (Biomatters) and assembled to the reference chromosome MG1655 (GenBank Accession Number 000913.2). The assembly process was set to medium/low sensitivity on Geneious, with the following parameters: 10% gaps allowed per read; word length of 18; index word length of 13; words repeated more than 12 times ignored; 20% maximum mismatches per read; and maximum ambiguity of 4 PGCGROWTHCONDITIONS
BAM files of the resulting assembly data were exported to JMP Genomics (SAS).  TMM normalization and ANOVA analysis of the read samples were conducted in JMP Genomics PGCGROWTHCONDITIONS
Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C. PGCGROWTHCONDITIONS
Cells were grown to approximately mid-log phase (OD560 = approximately 0.5) in LB. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype: mfd- PGCGROWTHCONDITIONS
mfd_2 PGCGROWTHCONDITIONS
MG1655 pCA24N and MG1655 pCA24N-Mfd cells were grown to an OD560 of approximately 0.25 and treated with 100 μM IPTG for 1 hour. PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
Read coverage maps and RPKM data was subsequently generated by Geneious. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads (approximately 13 to 25 million per sample) were imported into Geneious Pro (Biomatters) and assembled to the reference chromosome MG1655 (GenBank Accession Number 000913.2). The assembly process was set to medium/low sensitivity on Geneious, with the following parameters: 10% gaps allowed per read; word length of 18; index word length of 13; words repeated more than 12 times ignored; 20% maximum mismatches per read; and maximum ambiguity of 4 PGCGROWTHCONDITIONS
BAM files of the resulting assembly data were exported to JMP Genomics (SAS).  TMM normalization and ANOVA analysis of the read samples were conducted in JMP Genomics PGCGROWTHCONDITIONS
Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C. PGCGROWTHCONDITIONS
Cells were grown to approximately mid-log phase (OD560 = approximately 0.5) in LB. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype: mfd- PGCGROWTHCONDITIONS
mfd_3 PGCGROWTHCONDITIONS
MG1655 pCA24N and MG1655 pCA24N-Mfd cells were grown to an OD560 of approximately 0.25 and treated with 100 μM IPTG for 1 hour. PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
Read coverage maps and RPKM data was subsequently generated by Geneious. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads (approximately 13 to 25 million per sample) were imported into Geneious Pro (Biomatters) and assembled to the reference chromosome MG1655 (GenBank Accession Number 000913.2). The assembly process was set to medium/low sensitivity on Geneious, with the following parameters: 10% gaps allowed per read; word length of 18; index word length of 13; words repeated more than 12 times ignored; 20% maximum mismatches per read; and maximum ambiguity of 4 PGCGROWTHCONDITIONS
BAM files of the resulting assembly data were exported to JMP Genomics (SAS).  TMM normalization and ANOVA analysis of the read samples were conducted in JMP Genomics PGCGROWTHCONDITIONS
Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C. PGCGROWTHCONDITIONS
Cells were grown to approximately mid-log phase (OD560 = approximately 0.5) in LB. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype: Wildtype with vector PGCGROWTHCONDITIONS
MG1655 pCA24N and MG1655 pCA24N-Mfd cells were grown to an OD560 of approximately 0.25 and treated with 100 μM IPTG for 1 hour. PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
MG1655_vector_1 PGCGROWTHCONDITIONS
Read coverage maps and RPKM data was subsequently generated by Geneious. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads (approximately 13 to 25 million per sample) were imported into Geneious Pro (Biomatters) and assembled to the reference chromosome MG1655 (GenBank Accession Number 000913.2). The assembly process was set to medium/low sensitivity on Geneious, with the following parameters: 10% gaps allowed per read; word length of 18; index word length of 13; words repeated more than 12 times ignored; 20% maximum mismatches per read; and maximum ambiguity of 4 PGCGROWTHCONDITIONS
BAM files of the resulting assembly data were exported to JMP Genomics (SAS).  TMM normalization and ANOVA analysis of the read samples were conducted in JMP Genomics PGCGROWTHCONDITIONS
Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C. PGCGROWTHCONDITIONS
Cells were grown to approximately mid-log phase (OD560 = approximately 0.5) in LB. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype: Wildtype with vector PGCGROWTHCONDITIONS
MG1655 pCA24N and MG1655 pCA24N-Mfd cells were grown to an OD560 of approximately 0.25 and treated with 100 μM IPTG for 1 hour. PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
MG1655_vector_2 PGCGROWTHCONDITIONS
Read coverage maps and RPKM data was subsequently generated by Geneious. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads (approximately 13 to 25 million per sample) were imported into Geneious Pro (Biomatters) and assembled to the reference chromosome MG1655 (GenBank Accession Number 000913.2). The assembly process was set to medium/low sensitivity on Geneious, with the following parameters: 10% gaps allowed per read; word length of 18; index word length of 13; words repeated more than 12 times ignored; 20% maximum mismatches per read; and maximum ambiguity of 4 PGCGROWTHCONDITIONS
BAM files of the resulting assembly data were exported to JMP Genomics (SAS).  TMM normalization and ANOVA analysis of the read samples were conducted in JMP Genomics PGCGROWTHCONDITIONS
Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C. PGCGROWTHCONDITIONS
Cells were grown to approximately mid-log phase (OD560 = approximately 0.5) in LB. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype: Mfd++ PGCGROWTHCONDITIONS
MFD++_1 PGCGROWTHCONDITIONS
MG1655 pCA24N and MG1655 pCA24N-Mfd cells were grown to an OD560 of approximately 0.25 and treated with 100 μM IPTG for 1 hour. PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
Read coverage maps and RPKM data was subsequently generated by Geneious. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads (approximately 13 to 25 million per sample) were imported into Geneious Pro (Biomatters) and assembled to the reference chromosome MG1655 (GenBank Accession Number 000913.2). The assembly process was set to medium/low sensitivity on Geneious, with the following parameters: 10% gaps allowed per read; word length of 18; index word length of 13; words repeated more than 12 times ignored; 20% maximum mismatches per read; and maximum ambiguity of 4 PGCGROWTHCONDITIONS
BAM files of the resulting assembly data were exported to JMP Genomics (SAS).  TMM normalization and ANOVA analysis of the read samples were conducted in JMP Genomics PGCGROWTHCONDITIONS
Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C. PGCGROWTHCONDITIONS
Cells were grown to approximately mid-log phase (OD560 = approximately 0.5) in LB. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
genotype: Mfd++ PGCGROWTHCONDITIONS
MFD++_2 PGCGROWTHCONDITIONS
MG1655 pCA24N and MG1655 pCA24N-Mfd cells were grown to an OD560 of approximately 0.25 and treated with 100 μM IPTG for 1 hour. PGCGROWTHCONDITIONS
MG1655 PGCGROWTHCONDITIONS
Read coverage maps and RPKM data was subsequently generated by Geneious. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequencing reads (approximately 13 to 25 million per sample) were imported into Geneious Pro (Biomatters) and assembled to the reference chromosome MG1655 (GenBank Accession Number 000913.2). The assembly process was set to medium/low sensitivity on Geneious, with the following parameters: 10% gaps allowed per read; word length of 18; index word length of 13; words repeated more than 12 times ignored; 20% maximum mismatches per read; and maximum ambiguity of 4 PGCGROWTHCONDITIONS
17.3A_Space_25 PGCGROWTHCONDITIONS
17.3A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Four ml of the bacterial suspension in RNALater II and Medium E growth medium were spun down at 200g for 5 min. The supernatant was discarded and the pellet were resuspended in 200ul PBS and mixed by pipetting. 100ul aliquots were taken out for DNA and RNA extraction from the same sample. RNA extraction was done using Qiagen RNeasy mini kit (Qiagen, Hilden, Germany) with on-column DNase digestion. Final elution was made in 30 μL dH2O. The concentration and integrity of the total RNA was estimated by Quant-iT™ RiboGreen® RNA Assay Kit  (ThermoFisher Scientific, Waltham, MA), and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA), respectively. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (DH10B) PGCGROWTHCONDITIONS
gentamycin concentration (ug/ml): 25 PGCGROWTHCONDITIONS
location: Space PGCGROWTHCONDITIONS
Nineteen hours after experiment start, antibiotic (Gentamicin Sulfate (MP Biomedical, Cat No. 1676045, Santa Ana, CA, USA)) was introducing into the cultures. Antibiotic concentration varied from one sample to the next from 0 to 150 ug/mL in 25 ug/mL steps. Thirty hours later, samples were fixed in RNA Later II ((ACROS, Cat. No. 41678, New Jersey, USA)). Samples were stored at -75C until return to Earth for analyses. PGCGROWTHCONDITIONS
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Data-analysis was performed using the CLC Genomics Workbench (Version 7.5.1, CLC Bio, Aarhus, Denmark). The reference genome Escherichia coli (DH10B) sequence was downloaded from the UCSC genome browser. For read mapping, the following parameters were used: mismatch cost = 2, insertion and deletion cost = 3, length fraction: 0.8, similarity fraction = 0.8, global alignment = no, auto-detect paired distances = yes. Samples were grouped and differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions. PGCGROWTHCONDITIONS
Ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold (Yeast) kit (Epicenter, Madison, WI) using manufacturer's recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and adapter ligation. Post-ligated materials were individually barcoded with primers and amplified through 12 cycles of PCR. Final library quantity was assessed by Quant-iT™ PicoGreen® dsDNA Assay Kit and the library quality was estimated on LabChip® GX (Caliper, PerkinElmer, Waltham, MA). Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5 nM and pooled equimolar prior to clustering. Paired-End (PE) sequencing was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc.). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were sent to the International Space Station at 4C in FPAs, as described above. Temperature was increased to 37C and 23 hours later, the experiment was started by introducing the inoculum (E. coli ATCC 4157) into the growth medium (Medium E as described in Vogel & Bonner (1956) supplemented with 5 g/L glucose), yielding 3.25 mL of a culture with a starting cell concentration of 1.22e6 cell/mL. PGCGROWTHCONDITIONS
strain: ATCC 4157 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file include RPKM values for each Sample PGCGROWTHCONDITIONS
1.4A_Space_25 PGCGROWTHCONDITIONS
1.4A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Four ml of the bacterial suspension in RNALater II and Medium E growth medium were spun down at 200g for 5 min. The supernatant was discarded and the pellet were resuspended in 200ul PBS and mixed by pipetting. 100ul aliquots were taken out for DNA and RNA extraction from the same sample. RNA extraction was done using Qiagen RNeasy mini kit (Qiagen, Hilden, Germany) with on-column DNase digestion. Final elution was made in 30 μL dH2O. The concentration and integrity of the total RNA was estimated by Quant-iT™ RiboGreen® RNA Assay Kit  (ThermoFisher Scientific, Waltham, MA), and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA), respectively. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (DH10B) PGCGROWTHCONDITIONS
gentamycin concentration (ug/ml): 25 PGCGROWTHCONDITIONS
location: Space PGCGROWTHCONDITIONS
Nineteen hours after experiment start, antibiotic (Gentamicin Sulfate (MP Biomedical, Cat No. 1676045, Santa Ana, CA, USA)) was introducing into the cultures. Antibiotic concentration varied from one sample to the next from 0 to 150 ug/mL in 25 ug/mL steps. Thirty hours later, samples were fixed in RNA Later II ((ACROS, Cat. No. 41678, New Jersey, USA)). Samples were stored at -75C until return to Earth for analyses. PGCGROWTHCONDITIONS
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Data-analysis was performed using the CLC Genomics Workbench (Version 7.5.1, CLC Bio, Aarhus, Denmark). The reference genome Escherichia coli (DH10B) sequence was downloaded from the UCSC genome browser. For read mapping, the following parameters were used: mismatch cost = 2, insertion and deletion cost = 3, length fraction: 0.8, similarity fraction = 0.8, global alignment = no, auto-detect paired distances = yes. Samples were grouped and differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions. PGCGROWTHCONDITIONS
Ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold (Yeast) kit (Epicenter, Madison, WI) using manufacturer's recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and adapter ligation. Post-ligated materials were individually barcoded with primers and amplified through 12 cycles of PCR. Final library quantity was assessed by Quant-iT™ PicoGreen® dsDNA Assay Kit and the library quality was estimated on LabChip® GX (Caliper, PerkinElmer, Waltham, MA). Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5 nM and pooled equimolar prior to clustering. Paired-End (PE) sequencing was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc.). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were sent to the International Space Station at 4C in FPAs, as described above. Temperature was increased to 37C and 23 hours later, the experiment was started by introducing the inoculum (E. coli ATCC 4157) into the growth medium (Medium E as described in Vogel & Bonner (1956) supplemented with 5 g/L glucose), yielding 3.25 mL of a culture with a starting cell concentration of 1.22e6 cell/mL. PGCGROWTHCONDITIONS
strain: ATCC 4157 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file include RPKM values for each Sample PGCGROWTHCONDITIONS
17.5A_Space_50 PGCGROWTHCONDITIONS
17.5A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Four ml of the bacterial suspension in RNALater II and Medium E growth medium were spun down at 200g for 5 min. The supernatant was discarded and the pellet were resuspended in 200ul PBS and mixed by pipetting. 100ul aliquots were taken out for DNA and RNA extraction from the same sample. RNA extraction was done using Qiagen RNeasy mini kit (Qiagen, Hilden, Germany) with on-column DNase digestion. Final elution was made in 30 μL dH2O. The concentration and integrity of the total RNA was estimated by Quant-iT™ RiboGreen® RNA Assay Kit  (ThermoFisher Scientific, Waltham, MA), and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA), respectively. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (DH10B) PGCGROWTHCONDITIONS
gentamycin concentration (ug/ml): 50 PGCGROWTHCONDITIONS
location: Space PGCGROWTHCONDITIONS
Nineteen hours after experiment start, antibiotic (Gentamicin Sulfate (MP Biomedical, Cat No. 1676045, Santa Ana, CA, USA)) was introducing into the cultures. Antibiotic concentration varied from one sample to the next from 0 to 150 ug/mL in 25 ug/mL steps. Thirty hours later, samples were fixed in RNA Later II ((ACROS, Cat. No. 41678, New Jersey, USA)). Samples were stored at -75C until return to Earth for analyses. PGCGROWTHCONDITIONS
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Data-analysis was performed using the CLC Genomics Workbench (Version 7.5.1, CLC Bio, Aarhus, Denmark). The reference genome Escherichia coli (DH10B) sequence was downloaded from the UCSC genome browser. For read mapping, the following parameters were used: mismatch cost = 2, insertion and deletion cost = 3, length fraction: 0.8, similarity fraction = 0.8, global alignment = no, auto-detect paired distances = yes. Samples were grouped and differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions. PGCGROWTHCONDITIONS
Ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold (Yeast) kit (Epicenter, Madison, WI) using manufacturer's recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and adapter ligation. Post-ligated materials were individually barcoded with primers and amplified through 12 cycles of PCR. Final library quantity was assessed by Quant-iT™ PicoGreen® dsDNA Assay Kit and the library quality was estimated on LabChip® GX (Caliper, PerkinElmer, Waltham, MA). Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5 nM and pooled equimolar prior to clustering. Paired-End (PE) sequencing was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc.). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were sent to the International Space Station at 4C in FPAs, as described above. Temperature was increased to 37C and 23 hours later, the experiment was started by introducing the inoculum (E. coli ATCC 4157) into the growth medium (Medium E as described in Vogel & Bonner (1956) supplemented with 5 g/L glucose), yielding 3.25 mL of a culture with a starting cell concentration of 1.22e6 cell/mL. PGCGROWTHCONDITIONS
strain: ATCC 4157 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file include RPKM values for each Sample PGCGROWTHCONDITIONS
1.6A_Space_50 PGCGROWTHCONDITIONS
1.6A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Four ml of the bacterial suspension in RNALater II and Medium E growth medium were spun down at 200g for 5 min. The supernatant was discarded and the pellet were resuspended in 200ul PBS and mixed by pipetting. 100ul aliquots were taken out for DNA and RNA extraction from the same sample. RNA extraction was done using Qiagen RNeasy mini kit (Qiagen, Hilden, Germany) with on-column DNase digestion. Final elution was made in 30 μL dH2O. The concentration and integrity of the total RNA was estimated by Quant-iT™ RiboGreen® RNA Assay Kit  (ThermoFisher Scientific, Waltham, MA), and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA), respectively. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (DH10B) PGCGROWTHCONDITIONS
gentamycin concentration (ug/ml): 50 PGCGROWTHCONDITIONS
location: Space PGCGROWTHCONDITIONS
Nineteen hours after experiment start, antibiotic (Gentamicin Sulfate (MP Biomedical, Cat No. 1676045, Santa Ana, CA, USA)) was introducing into the cultures. Antibiotic concentration varied from one sample to the next from 0 to 150 ug/mL in 25 ug/mL steps. Thirty hours later, samples were fixed in RNA Later II ((ACROS, Cat. No. 41678, New Jersey, USA)). Samples were stored at -75C until return to Earth for analyses. PGCGROWTHCONDITIONS
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Data-analysis was performed using the CLC Genomics Workbench (Version 7.5.1, CLC Bio, Aarhus, Denmark). The reference genome Escherichia coli (DH10B) sequence was downloaded from the UCSC genome browser. For read mapping, the following parameters were used: mismatch cost = 2, insertion and deletion cost = 3, length fraction: 0.8, similarity fraction = 0.8, global alignment = no, auto-detect paired distances = yes. Samples were grouped and differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions. PGCGROWTHCONDITIONS
Ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold (Yeast) kit (Epicenter, Madison, WI) using manufacturer's recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and adapter ligation. Post-ligated materials were individually barcoded with primers and amplified through 12 cycles of PCR. Final library quantity was assessed by Quant-iT™ PicoGreen® dsDNA Assay Kit and the library quality was estimated on LabChip® GX (Caliper, PerkinElmer, Waltham, MA). Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5 nM and pooled equimolar prior to clustering. Paired-End (PE) sequencing was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc.). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were sent to the International Space Station at 4C in FPAs, as described above. Temperature was increased to 37C and 23 hours later, the experiment was started by introducing the inoculum (E. coli ATCC 4157) into the growth medium (Medium E as described in Vogel & Bonner (1956) supplemented with 5 g/L glucose), yielding 3.25 mL of a culture with a starting cell concentration of 1.22e6 cell/mL. PGCGROWTHCONDITIONS
strain: ATCC 4157 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file include RPKM values for each Sample PGCGROWTHCONDITIONS
17.6A_Space_50 PGCGROWTHCONDITIONS
17.6A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Four ml of the bacterial suspension in RNALater II and Medium E growth medium were spun down at 200g for 5 min. The supernatant was discarded and the pellet were resuspended in 200ul PBS and mixed by pipetting. 100ul aliquots were taken out for DNA and RNA extraction from the same sample. RNA extraction was done using Qiagen RNeasy mini kit (Qiagen, Hilden, Germany) with on-column DNase digestion. Final elution was made in 30 μL dH2O. The concentration and integrity of the total RNA was estimated by Quant-iT™ RiboGreen® RNA Assay Kit  (ThermoFisher Scientific, Waltham, MA), and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA), respectively. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (DH10B) PGCGROWTHCONDITIONS
gentamycin concentration (ug/ml): 50 PGCGROWTHCONDITIONS
location: Space PGCGROWTHCONDITIONS
Nineteen hours after experiment start, antibiotic (Gentamicin Sulfate (MP Biomedical, Cat No. 1676045, Santa Ana, CA, USA)) was introducing into the cultures. Antibiotic concentration varied from one sample to the next from 0 to 150 ug/mL in 25 ug/mL steps. Thirty hours later, samples were fixed in RNA Later II ((ACROS, Cat. No. 41678, New Jersey, USA)). Samples were stored at -75C until return to Earth for analyses. PGCGROWTHCONDITIONS
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Data-analysis was performed using the CLC Genomics Workbench (Version 7.5.1, CLC Bio, Aarhus, Denmark). The reference genome Escherichia coli (DH10B) sequence was downloaded from the UCSC genome browser. For read mapping, the following parameters were used: mismatch cost = 2, insertion and deletion cost = 3, length fraction: 0.8, similarity fraction = 0.8, global alignment = no, auto-detect paired distances = yes. Samples were grouped and differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions. PGCGROWTHCONDITIONS
Ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold (Yeast) kit (Epicenter, Madison, WI) using manufacturer's recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and adapter ligation. Post-ligated materials were individually barcoded with primers and amplified through 12 cycles of PCR. Final library quantity was assessed by Quant-iT™ PicoGreen® dsDNA Assay Kit and the library quality was estimated on LabChip® GX (Caliper, PerkinElmer, Waltham, MA). Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5 nM and pooled equimolar prior to clustering. Paired-End (PE) sequencing was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc.). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were sent to the International Space Station at 4C in FPAs, as described above. Temperature was increased to 37C and 23 hours later, the experiment was started by introducing the inoculum (E. coli ATCC 4157) into the growth medium (Medium E as described in Vogel & Bonner (1956) supplemented with 5 g/L glucose), yielding 3.25 mL of a culture with a starting cell concentration of 1.22e6 cell/mL. PGCGROWTHCONDITIONS
strain: ATCC 4157 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file include RPKM values for each Sample PGCGROWTHCONDITIONS
18.3A_Space_75 PGCGROWTHCONDITIONS
18.3A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Four ml of the bacterial suspension in RNALater II and Medium E growth medium were spun down at 200g for 5 min. The supernatant was discarded and the pellet were resuspended in 200ul PBS and mixed by pipetting. 100ul aliquots were taken out for DNA and RNA extraction from the same sample. RNA extraction was done using Qiagen RNeasy mini kit (Qiagen, Hilden, Germany) with on-column DNase digestion. Final elution was made in 30 μL dH2O. The concentration and integrity of the total RNA was estimated by Quant-iT™ RiboGreen® RNA Assay Kit  (ThermoFisher Scientific, Waltham, MA), and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA), respectively. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (DH10B) PGCGROWTHCONDITIONS
gentamycin concentration (ug/ml): 75 PGCGROWTHCONDITIONS
location: Space PGCGROWTHCONDITIONS
Nineteen hours after experiment start, antibiotic (Gentamicin Sulfate (MP Biomedical, Cat No. 1676045, Santa Ana, CA, USA)) was introducing into the cultures. Antibiotic concentration varied from one sample to the next from 0 to 150 ug/mL in 25 ug/mL steps. Thirty hours later, samples were fixed in RNA Later II ((ACROS, Cat. No. 41678, New Jersey, USA)). Samples were stored at -75C until return to Earth for analyses. PGCGROWTHCONDITIONS
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Data-analysis was performed using the CLC Genomics Workbench (Version 7.5.1, CLC Bio, Aarhus, Denmark). The reference genome Escherichia coli (DH10B) sequence was downloaded from the UCSC genome browser. For read mapping, the following parameters were used: mismatch cost = 2, insertion and deletion cost = 3, length fraction: 0.8, similarity fraction = 0.8, global alignment = no, auto-detect paired distances = yes. Samples were grouped and differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions. PGCGROWTHCONDITIONS
Ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold (Yeast) kit (Epicenter, Madison, WI) using manufacturer's recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and adapter ligation. Post-ligated materials were individually barcoded with primers and amplified through 12 cycles of PCR. Final library quantity was assessed by Quant-iT™ PicoGreen® dsDNA Assay Kit and the library quality was estimated on LabChip® GX (Caliper, PerkinElmer, Waltham, MA). Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5 nM and pooled equimolar prior to clustering. Paired-End (PE) sequencing was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc.). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were sent to the International Space Station at 4C in FPAs, as described above. Temperature was increased to 37C and 23 hours later, the experiment was started by introducing the inoculum (E. coli ATCC 4157) into the growth medium (Medium E as described in Vogel & Bonner (1956) supplemented with 5 g/L glucose), yielding 3.25 mL of a culture with a starting cell concentration of 1.22e6 cell/mL. PGCGROWTHCONDITIONS
strain: ATCC 4157 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file include RPKM values for each Sample PGCGROWTHCONDITIONS
2.4A_Space_75 PGCGROWTHCONDITIONS
2.4A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Four ml of the bacterial suspension in RNALater II and Medium E growth medium were spun down at 200g for 5 min. The supernatant was discarded and the pellet were resuspended in 200ul PBS and mixed by pipetting. 100ul aliquots were taken out for DNA and RNA extraction from the same sample. RNA extraction was done using Qiagen RNeasy mini kit (Qiagen, Hilden, Germany) with on-column DNase digestion. Final elution was made in 30 μL dH2O. The concentration and integrity of the total RNA was estimated by Quant-iT™ RiboGreen® RNA Assay Kit  (ThermoFisher Scientific, Waltham, MA), and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA), respectively. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (DH10B) PGCGROWTHCONDITIONS
gentamycin concentration (ug/ml): 75 PGCGROWTHCONDITIONS
location: Space PGCGROWTHCONDITIONS
Nineteen hours after experiment start, antibiotic (Gentamicin Sulfate (MP Biomedical, Cat No. 1676045, Santa Ana, CA, USA)) was introducing into the cultures. Antibiotic concentration varied from one sample to the next from 0 to 150 ug/mL in 25 ug/mL steps. Thirty hours later, samples were fixed in RNA Later II ((ACROS, Cat. No. 41678, New Jersey, USA)). Samples were stored at -75C until return to Earth for analyses. PGCGROWTHCONDITIONS
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Data-analysis was performed using the CLC Genomics Workbench (Version 7.5.1, CLC Bio, Aarhus, Denmark). The reference genome Escherichia coli (DH10B) sequence was downloaded from the UCSC genome browser. For read mapping, the following parameters were used: mismatch cost = 2, insertion and deletion cost = 3, length fraction: 0.8, similarity fraction = 0.8, global alignment = no, auto-detect paired distances = yes. Samples were grouped and differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions. PGCGROWTHCONDITIONS
Ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold (Yeast) kit (Epicenter, Madison, WI) using manufacturer's recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and adapter ligation. Post-ligated materials were individually barcoded with primers and amplified through 12 cycles of PCR. Final library quantity was assessed by Quant-iT™ PicoGreen® dsDNA Assay Kit and the library quality was estimated on LabChip® GX (Caliper, PerkinElmer, Waltham, MA). Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5 nM and pooled equimolar prior to clustering. Paired-End (PE) sequencing was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc.). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were sent to the International Space Station at 4C in FPAs, as described above. Temperature was increased to 37C and 23 hours later, the experiment was started by introducing the inoculum (E. coli ATCC 4157) into the growth medium (Medium E as described in Vogel & Bonner (1956) supplemented with 5 g/L glucose), yielding 3.25 mL of a culture with a starting cell concentration of 1.22e6 cell/mL. PGCGROWTHCONDITIONS
strain: ATCC 4157 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file include RPKM values for each Sample PGCGROWTHCONDITIONS
1.1A_Earth_25 PGCGROWTHCONDITIONS
1.1A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Four ml of the bacterial suspension in RNALater II and Medium E growth medium were spun down at 200g for 5 min. The supernatant was discarded and the pellet were resuspended in 200ul PBS and mixed by pipetting. 100ul aliquots were taken out for DNA and RNA extraction from the same sample. RNA extraction was done using Qiagen RNeasy mini kit (Qiagen, Hilden, Germany) with on-column DNase digestion. Final elution was made in 30 μL dH2O. The concentration and integrity of the total RNA was estimated by Quant-iT™ RiboGreen® RNA Assay Kit  (ThermoFisher Scientific, Waltham, MA), and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA), respectively. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (DH10B) PGCGROWTHCONDITIONS
gentamycin concentration (ug/ml): 25 PGCGROWTHCONDITIONS
location: Earth PGCGROWTHCONDITIONS
Nineteen hours after experiment start, antibiotic (Gentamicin Sulfate (MP Biomedical, Cat No. 1676045, Santa Ana, CA, USA)) was introducing into the cultures. Antibiotic concentration varied from one sample to the next from 0 to 150 ug/mL in 25 ug/mL steps. Thirty hours later, samples were fixed in RNA Later II ((ACROS, Cat. No. 41678, New Jersey, USA)). Samples were stored at -75C until return to Earth for analyses. PGCGROWTHCONDITIONS
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Data-analysis was performed using the CLC Genomics Workbench (Version 7.5.1, CLC Bio, Aarhus, Denmark). The reference genome Escherichia coli (DH10B) sequence was downloaded from the UCSC genome browser. For read mapping, the following parameters were used: mismatch cost = 2, insertion and deletion cost = 3, length fraction: 0.8, similarity fraction = 0.8, global alignment = no, auto-detect paired distances = yes. Samples were grouped and differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions. PGCGROWTHCONDITIONS
Ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold (Yeast) kit (Epicenter, Madison, WI) using manufacturer's recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and adapter ligation. Post-ligated materials were individually barcoded with primers and amplified through 12 cycles of PCR. Final library quantity was assessed by Quant-iT™ PicoGreen® dsDNA Assay Kit and the library quality was estimated on LabChip® GX (Caliper, PerkinElmer, Waltham, MA). Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5 nM and pooled equimolar prior to clustering. Paired-End (PE) sequencing was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc.). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were sent to the International Space Station at 4C in FPAs, as described above. Temperature was increased to 37C and 23 hours later, the experiment was started by introducing the inoculum (E. coli ATCC 4157) into the growth medium (Medium E as described in Vogel & Bonner (1956) supplemented with 5 g/L glucose), yielding 3.25 mL of a culture with a starting cell concentration of 1.22e6 cell/mL. PGCGROWTHCONDITIONS
strain: ATCC 4157 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file include RPKM values for each Sample PGCGROWTHCONDITIONS
17.2A_Earth_25 PGCGROWTHCONDITIONS
17.2A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Four ml of the bacterial suspension in RNALater II and Medium E growth medium were spun down at 200g for 5 min. The supernatant was discarded and the pellet were resuspended in 200ul PBS and mixed by pipetting. 100ul aliquots were taken out for DNA and RNA extraction from the same sample. RNA extraction was done using Qiagen RNeasy mini kit (Qiagen, Hilden, Germany) with on-column DNase digestion. Final elution was made in 30 μL dH2O. The concentration and integrity of the total RNA was estimated by Quant-iT™ RiboGreen® RNA Assay Kit  (ThermoFisher Scientific, Waltham, MA), and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA), respectively. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (DH10B) PGCGROWTHCONDITIONS
gentamycin concentration (ug/ml): 25 PGCGROWTHCONDITIONS
location: Earth PGCGROWTHCONDITIONS
Nineteen hours after experiment start, antibiotic (Gentamicin Sulfate (MP Biomedical, Cat No. 1676045, Santa Ana, CA, USA)) was introducing into the cultures. Antibiotic concentration varied from one sample to the next from 0 to 150 ug/mL in 25 ug/mL steps. Thirty hours later, samples were fixed in RNA Later II ((ACROS, Cat. No. 41678, New Jersey, USA)). Samples were stored at -75C until return to Earth for analyses. PGCGROWTHCONDITIONS
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Data-analysis was performed using the CLC Genomics Workbench (Version 7.5.1, CLC Bio, Aarhus, Denmark). The reference genome Escherichia coli (DH10B) sequence was downloaded from the UCSC genome browser. For read mapping, the following parameters were used: mismatch cost = 2, insertion and deletion cost = 3, length fraction: 0.8, similarity fraction = 0.8, global alignment = no, auto-detect paired distances = yes. Samples were grouped and differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions. PGCGROWTHCONDITIONS
Ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold (Yeast) kit (Epicenter, Madison, WI) using manufacturer's recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and adapter ligation. Post-ligated materials were individually barcoded with primers and amplified through 12 cycles of PCR. Final library quantity was assessed by Quant-iT™ PicoGreen® dsDNA Assay Kit and the library quality was estimated on LabChip® GX (Caliper, PerkinElmer, Waltham, MA). Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5 nM and pooled equimolar prior to clustering. Paired-End (PE) sequencing was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc.). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were sent to the International Space Station at 4C in FPAs, as described above. Temperature was increased to 37C and 23 hours later, the experiment was started by introducing the inoculum (E. coli ATCC 4157) into the growth medium (Medium E as described in Vogel & Bonner (1956) supplemented with 5 g/L glucose), yielding 3.25 mL of a culture with a starting cell concentration of 1.22e6 cell/mL. PGCGROWTHCONDITIONS
strain: ATCC 4157 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file include RPKM values for each Sample PGCGROWTHCONDITIONS
1.3A_Earth_25 PGCGROWTHCONDITIONS
1.3A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Four ml of the bacterial suspension in RNALater II and Medium E growth medium were spun down at 200g for 5 min. The supernatant was discarded and the pellet were resuspended in 200ul PBS and mixed by pipetting. 100ul aliquots were taken out for DNA and RNA extraction from the same sample. RNA extraction was done using Qiagen RNeasy mini kit (Qiagen, Hilden, Germany) with on-column DNase digestion. Final elution was made in 30 μL dH2O. The concentration and integrity of the total RNA was estimated by Quant-iT™ RiboGreen® RNA Assay Kit  (ThermoFisher Scientific, Waltham, MA), and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA), respectively. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (DH10B) PGCGROWTHCONDITIONS
gentamycin concentration (ug/ml): 25 PGCGROWTHCONDITIONS
location: Earth PGCGROWTHCONDITIONS
Nineteen hours after experiment start, antibiotic (Gentamicin Sulfate (MP Biomedical, Cat No. 1676045, Santa Ana, CA, USA)) was introducing into the cultures. Antibiotic concentration varied from one sample to the next from 0 to 150 ug/mL in 25 ug/mL steps. Thirty hours later, samples were fixed in RNA Later II ((ACROS, Cat. No. 41678, New Jersey, USA)). Samples were stored at -75C until return to Earth for analyses. PGCGROWTHCONDITIONS
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Data-analysis was performed using the CLC Genomics Workbench (Version 7.5.1, CLC Bio, Aarhus, Denmark). The reference genome Escherichia coli (DH10B) sequence was downloaded from the UCSC genome browser. For read mapping, the following parameters were used: mismatch cost = 2, insertion and deletion cost = 3, length fraction: 0.8, similarity fraction = 0.8, global alignment = no, auto-detect paired distances = yes. Samples were grouped and differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions. PGCGROWTHCONDITIONS
Ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold (Yeast) kit (Epicenter, Madison, WI) using manufacturer's recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and adapter ligation. Post-ligated materials were individually barcoded with primers and amplified through 12 cycles of PCR. Final library quantity was assessed by Quant-iT™ PicoGreen® dsDNA Assay Kit and the library quality was estimated on LabChip® GX (Caliper, PerkinElmer, Waltham, MA). Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5 nM and pooled equimolar prior to clustering. Paired-End (PE) sequencing was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc.). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were sent to the International Space Station at 4C in FPAs, as described above. Temperature was increased to 37C and 23 hours later, the experiment was started by introducing the inoculum (E. coli ATCC 4157) into the growth medium (Medium E as described in Vogel & Bonner (1956) supplemented with 5 g/L glucose), yielding 3.25 mL of a culture with a starting cell concentration of 1.22e6 cell/mL. PGCGROWTHCONDITIONS
strain: ATCC 4157 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file include RPKM values for each Sample PGCGROWTHCONDITIONS
17.4A_Earth_25 PGCGROWTHCONDITIONS
17.4A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Four ml of the bacterial suspension in RNALater II and Medium E growth medium were spun down at 200g for 5 min. The supernatant was discarded and the pellet were resuspended in 200ul PBS and mixed by pipetting. 100ul aliquots were taken out for DNA and RNA extraction from the same sample. RNA extraction was done using Qiagen RNeasy mini kit (Qiagen, Hilden, Germany) with on-column DNase digestion. Final elution was made in 30 μL dH2O. The concentration and integrity of the total RNA was estimated by Quant-iT™ RiboGreen® RNA Assay Kit  (ThermoFisher Scientific, Waltham, MA), and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA), respectively. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (DH10B) PGCGROWTHCONDITIONS
gentamycin concentration (ug/ml): 25 PGCGROWTHCONDITIONS
location: Earth PGCGROWTHCONDITIONS
Nineteen hours after experiment start, antibiotic (Gentamicin Sulfate (MP Biomedical, Cat No. 1676045, Santa Ana, CA, USA)) was introducing into the cultures. Antibiotic concentration varied from one sample to the next from 0 to 150 ug/mL in 25 ug/mL steps. Thirty hours later, samples were fixed in RNA Later II ((ACROS, Cat. No. 41678, New Jersey, USA)). Samples were stored at -75C until return to Earth for analyses. PGCGROWTHCONDITIONS
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Data-analysis was performed using the CLC Genomics Workbench (Version 7.5.1, CLC Bio, Aarhus, Denmark). The reference genome Escherichia coli (DH10B) sequence was downloaded from the UCSC genome browser. For read mapping, the following parameters were used: mismatch cost = 2, insertion and deletion cost = 3, length fraction: 0.8, similarity fraction = 0.8, global alignment = no, auto-detect paired distances = yes. Samples were grouped and differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions. PGCGROWTHCONDITIONS
Ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold (Yeast) kit (Epicenter, Madison, WI) using manufacturer's recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and adapter ligation. Post-ligated materials were individually barcoded with primers and amplified through 12 cycles of PCR. Final library quantity was assessed by Quant-iT™ PicoGreen® dsDNA Assay Kit and the library quality was estimated on LabChip® GX (Caliper, PerkinElmer, Waltham, MA). Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5 nM and pooled equimolar prior to clustering. Paired-End (PE) sequencing was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc.). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were sent to the International Space Station at 4C in FPAs, as described above. Temperature was increased to 37C and 23 hours later, the experiment was started by introducing the inoculum (E. coli ATCC 4157) into the growth medium (Medium E as described in Vogel & Bonner (1956) supplemented with 5 g/L glucose), yielding 3.25 mL of a culture with a starting cell concentration of 1.22e6 cell/mL. PGCGROWTHCONDITIONS
strain: ATCC 4157 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file include RPKM values for each Sample PGCGROWTHCONDITIONS
1.5A_Earth_50 PGCGROWTHCONDITIONS
1.5A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Four ml of the bacterial suspension in RNALater II and Medium E growth medium were spun down at 200g for 5 min. The supernatant was discarded and the pellet were resuspended in 200ul PBS and mixed by pipetting. 100ul aliquots were taken out for DNA and RNA extraction from the same sample. RNA extraction was done using Qiagen RNeasy mini kit (Qiagen, Hilden, Germany) with on-column DNase digestion. Final elution was made in 30 μL dH2O. The concentration and integrity of the total RNA was estimated by Quant-iT™ RiboGreen® RNA Assay Kit  (ThermoFisher Scientific, Waltham, MA), and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA), respectively. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (DH10B) PGCGROWTHCONDITIONS
gentamycin concentration (ug/ml): 50 PGCGROWTHCONDITIONS
location: Earth PGCGROWTHCONDITIONS
Nineteen hours after experiment start, antibiotic (Gentamicin Sulfate (MP Biomedical, Cat No. 1676045, Santa Ana, CA, USA)) was introducing into the cultures. Antibiotic concentration varied from one sample to the next from 0 to 150 ug/mL in 25 ug/mL steps. Thirty hours later, samples were fixed in RNA Later II ((ACROS, Cat. No. 41678, New Jersey, USA)). Samples were stored at -75C until return to Earth for analyses. PGCGROWTHCONDITIONS
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Data-analysis was performed using the CLC Genomics Workbench (Version 7.5.1, CLC Bio, Aarhus, Denmark). The reference genome Escherichia coli (DH10B) sequence was downloaded from the UCSC genome browser. For read mapping, the following parameters were used: mismatch cost = 2, insertion and deletion cost = 3, length fraction: 0.8, similarity fraction = 0.8, global alignment = no, auto-detect paired distances = yes. Samples were grouped and differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions. PGCGROWTHCONDITIONS
Ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold (Yeast) kit (Epicenter, Madison, WI) using manufacturer's recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and adapter ligation. Post-ligated materials were individually barcoded with primers and amplified through 12 cycles of PCR. Final library quantity was assessed by Quant-iT™ PicoGreen® dsDNA Assay Kit and the library quality was estimated on LabChip® GX (Caliper, PerkinElmer, Waltham, MA). Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5 nM and pooled equimolar prior to clustering. Paired-End (PE) sequencing was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc.). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were sent to the International Space Station at 4C in FPAs, as described above. Temperature was increased to 37C and 23 hours later, the experiment was started by introducing the inoculum (E. coli ATCC 4157) into the growth medium (Medium E as described in Vogel & Bonner (1956) supplemented with 5 g/L glucose), yielding 3.25 mL of a culture with a starting cell concentration of 1.22e6 cell/mL. PGCGROWTHCONDITIONS
strain: ATCC 4157 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file include RPKM values for each Sample PGCGROWTHCONDITIONS
17.8A_Earth_50 PGCGROWTHCONDITIONS
17.8A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Four ml of the bacterial suspension in RNALater II and Medium E growth medium were spun down at 200g for 5 min. The supernatant was discarded and the pellet were resuspended in 200ul PBS and mixed by pipetting. 100ul aliquots were taken out for DNA and RNA extraction from the same sample. RNA extraction was done using Qiagen RNeasy mini kit (Qiagen, Hilden, Germany) with on-column DNase digestion. Final elution was made in 30 μL dH2O. The concentration and integrity of the total RNA was estimated by Quant-iT™ RiboGreen® RNA Assay Kit  (ThermoFisher Scientific, Waltham, MA), and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA), respectively. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (DH10B) PGCGROWTHCONDITIONS
gentamycin concentration (ug/ml): 50 PGCGROWTHCONDITIONS
location: Earth PGCGROWTHCONDITIONS
Nineteen hours after experiment start, antibiotic (Gentamicin Sulfate (MP Biomedical, Cat No. 1676045, Santa Ana, CA, USA)) was introducing into the cultures. Antibiotic concentration varied from one sample to the next from 0 to 150 ug/mL in 25 ug/mL steps. Thirty hours later, samples were fixed in RNA Later II ((ACROS, Cat. No. 41678, New Jersey, USA)). Samples were stored at -75C until return to Earth for analyses. PGCGROWTHCONDITIONS
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Data-analysis was performed using the CLC Genomics Workbench (Version 7.5.1, CLC Bio, Aarhus, Denmark). The reference genome Escherichia coli (DH10B) sequence was downloaded from the UCSC genome browser. For read mapping, the following parameters were used: mismatch cost = 2, insertion and deletion cost = 3, length fraction: 0.8, similarity fraction = 0.8, global alignment = no, auto-detect paired distances = yes. Samples were grouped and differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions. PGCGROWTHCONDITIONS
Ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold (Yeast) kit (Epicenter, Madison, WI) using manufacturer's recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and adapter ligation. Post-ligated materials were individually barcoded with primers and amplified through 12 cycles of PCR. Final library quantity was assessed by Quant-iT™ PicoGreen® dsDNA Assay Kit and the library quality was estimated on LabChip® GX (Caliper, PerkinElmer, Waltham, MA). Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5 nM and pooled equimolar prior to clustering. Paired-End (PE) sequencing was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc.). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were sent to the International Space Station at 4C in FPAs, as described above. Temperature was increased to 37C and 23 hours later, the experiment was started by introducing the inoculum (E. coli ATCC 4157) into the growth medium (Medium E as described in Vogel & Bonner (1956) supplemented with 5 g/L glucose), yielding 3.25 mL of a culture with a starting cell concentration of 1.22e6 cell/mL. PGCGROWTHCONDITIONS
strain: ATCC 4157 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file include RPKM values for each Sample PGCGROWTHCONDITIONS
2.1A_Earth_75 PGCGROWTHCONDITIONS
2.1A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Four ml of the bacterial suspension in RNALater II and Medium E growth medium were spun down at 200g for 5 min. The supernatant was discarded and the pellet were resuspended in 200ul PBS and mixed by pipetting. 100ul aliquots were taken out for DNA and RNA extraction from the same sample. RNA extraction was done using Qiagen RNeasy mini kit (Qiagen, Hilden, Germany) with on-column DNase digestion. Final elution was made in 30 μL dH2O. The concentration and integrity of the total RNA was estimated by Quant-iT™ RiboGreen® RNA Assay Kit  (ThermoFisher Scientific, Waltham, MA), and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA), respectively. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (DH10B) PGCGROWTHCONDITIONS
gentamycin concentration (ug/ml): 75 PGCGROWTHCONDITIONS
location: Earth PGCGROWTHCONDITIONS
Nineteen hours after experiment start, antibiotic (Gentamicin Sulfate (MP Biomedical, Cat No. 1676045, Santa Ana, CA, USA)) was introducing into the cultures. Antibiotic concentration varied from one sample to the next from 0 to 150 ug/mL in 25 ug/mL steps. Thirty hours later, samples were fixed in RNA Later II ((ACROS, Cat. No. 41678, New Jersey, USA)). Samples were stored at -75C until return to Earth for analyses. PGCGROWTHCONDITIONS
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Data-analysis was performed using the CLC Genomics Workbench (Version 7.5.1, CLC Bio, Aarhus, Denmark). The reference genome Escherichia coli (DH10B) sequence was downloaded from the UCSC genome browser. For read mapping, the following parameters were used: mismatch cost = 2, insertion and deletion cost = 3, length fraction: 0.8, similarity fraction = 0.8, global alignment = no, auto-detect paired distances = yes. Samples were grouped and differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions. PGCGROWTHCONDITIONS
Ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold (Yeast) kit (Epicenter, Madison, WI) using manufacturer's recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and adapter ligation. Post-ligated materials were individually barcoded with primers and amplified through 12 cycles of PCR. Final library quantity was assessed by Quant-iT™ PicoGreen® dsDNA Assay Kit and the library quality was estimated on LabChip® GX (Caliper, PerkinElmer, Waltham, MA). Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5 nM and pooled equimolar prior to clustering. Paired-End (PE) sequencing was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc.). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were sent to the International Space Station at 4C in FPAs, as described above. Temperature was increased to 37C and 23 hours later, the experiment was started by introducing the inoculum (E. coli ATCC 4157) into the growth medium (Medium E as described in Vogel & Bonner (1956) supplemented with 5 g/L glucose), yielding 3.25 mL of a culture with a starting cell concentration of 1.22e6 cell/mL. PGCGROWTHCONDITIONS
strain: ATCC 4157 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file include RPKM values for each Sample PGCGROWTHCONDITIONS
18.2A_Earth_75 PGCGROWTHCONDITIONS
18.2A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Four ml of the bacterial suspension in RNALater II and Medium E growth medium were spun down at 200g for 5 min. The supernatant was discarded and the pellet were resuspended in 200ul PBS and mixed by pipetting. 100ul aliquots were taken out for DNA and RNA extraction from the same sample. RNA extraction was done using Qiagen RNeasy mini kit (Qiagen, Hilden, Germany) with on-column DNase digestion. Final elution was made in 30 μL dH2O. The concentration and integrity of the total RNA was estimated by Quant-iT™ RiboGreen® RNA Assay Kit  (ThermoFisher Scientific, Waltham, MA), and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA), respectively. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (DH10B) PGCGROWTHCONDITIONS
gentamycin concentration (ug/ml): 75 PGCGROWTHCONDITIONS
location: Earth PGCGROWTHCONDITIONS
Nineteen hours after experiment start, antibiotic (Gentamicin Sulfate (MP Biomedical, Cat No. 1676045, Santa Ana, CA, USA)) was introducing into the cultures. Antibiotic concentration varied from one sample to the next from 0 to 150 ug/mL in 25 ug/mL steps. Thirty hours later, samples were fixed in RNA Later II ((ACROS, Cat. No. 41678, New Jersey, USA)). Samples were stored at -75C until return to Earth for analyses. PGCGROWTHCONDITIONS
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Data-analysis was performed using the CLC Genomics Workbench (Version 7.5.1, CLC Bio, Aarhus, Denmark). The reference genome Escherichia coli (DH10B) sequence was downloaded from the UCSC genome browser. For read mapping, the following parameters were used: mismatch cost = 2, insertion and deletion cost = 3, length fraction: 0.8, similarity fraction = 0.8, global alignment = no, auto-detect paired distances = yes. Samples were grouped and differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions. PGCGROWTHCONDITIONS
Ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold (Yeast) kit (Epicenter, Madison, WI) using manufacturer's recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and adapter ligation. Post-ligated materials were individually barcoded with primers and amplified through 12 cycles of PCR. Final library quantity was assessed by Quant-iT™ PicoGreen® dsDNA Assay Kit and the library quality was estimated on LabChip® GX (Caliper, PerkinElmer, Waltham, MA). Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5 nM and pooled equimolar prior to clustering. Paired-End (PE) sequencing was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc.). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were sent to the International Space Station at 4C in FPAs, as described above. Temperature was increased to 37C and 23 hours later, the experiment was started by introducing the inoculum (E. coli ATCC 4157) into the growth medium (Medium E as described in Vogel & Bonner (1956) supplemented with 5 g/L glucose), yielding 3.25 mL of a culture with a starting cell concentration of 1.22e6 cell/mL. PGCGROWTHCONDITIONS
strain: ATCC 4157 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file include RPKM values for each Sample PGCGROWTHCONDITIONS
2.3A_Earth_75 PGCGROWTHCONDITIONS
2.3A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Four ml of the bacterial suspension in RNALater II and Medium E growth medium were spun down at 200g for 5 min. The supernatant was discarded and the pellet were resuspended in 200ul PBS and mixed by pipetting. 100ul aliquots were taken out for DNA and RNA extraction from the same sample. RNA extraction was done using Qiagen RNeasy mini kit (Qiagen, Hilden, Germany) with on-column DNase digestion. Final elution was made in 30 μL dH2O. The concentration and integrity of the total RNA was estimated by Quant-iT™ RiboGreen® RNA Assay Kit  (ThermoFisher Scientific, Waltham, MA), and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA), respectively. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (DH10B) PGCGROWTHCONDITIONS
gentamycin concentration (ug/ml): 75 PGCGROWTHCONDITIONS
location: Earth PGCGROWTHCONDITIONS
Nineteen hours after experiment start, antibiotic (Gentamicin Sulfate (MP Biomedical, Cat No. 1676045, Santa Ana, CA, USA)) was introducing into the cultures. Antibiotic concentration varied from one sample to the next from 0 to 150 ug/mL in 25 ug/mL steps. Thirty hours later, samples were fixed in RNA Later II ((ACROS, Cat. No. 41678, New Jersey, USA)). Samples were stored at -75C until return to Earth for analyses. PGCGROWTHCONDITIONS
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Data-analysis was performed using the CLC Genomics Workbench (Version 7.5.1, CLC Bio, Aarhus, Denmark). The reference genome Escherichia coli (DH10B) sequence was downloaded from the UCSC genome browser. For read mapping, the following parameters were used: mismatch cost = 2, insertion and deletion cost = 3, length fraction: 0.8, similarity fraction = 0.8, global alignment = no, auto-detect paired distances = yes. Samples were grouped and differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions. PGCGROWTHCONDITIONS
Ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold (Yeast) kit (Epicenter, Madison, WI) using manufacturer's recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and adapter ligation. Post-ligated materials were individually barcoded with primers and amplified through 12 cycles of PCR. Final library quantity was assessed by Quant-iT™ PicoGreen® dsDNA Assay Kit and the library quality was estimated on LabChip® GX (Caliper, PerkinElmer, Waltham, MA). Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5 nM and pooled equimolar prior to clustering. Paired-End (PE) sequencing was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc.). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were sent to the International Space Station at 4C in FPAs, as described above. Temperature was increased to 37C and 23 hours later, the experiment was started by introducing the inoculum (E. coli ATCC 4157) into the growth medium (Medium E as described in Vogel & Bonner (1956) supplemented with 5 g/L glucose), yielding 3.25 mL of a culture with a starting cell concentration of 1.22e6 cell/mL. PGCGROWTHCONDITIONS
strain: ATCC 4157 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file include RPKM values for each Sample PGCGROWTHCONDITIONS
18.4A_Earth_75 PGCGROWTHCONDITIONS
18.4A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Four ml of the bacterial suspension in RNALater II and Medium E growth medium were spun down at 200g for 5 min. The supernatant was discarded and the pellet were resuspended in 200ul PBS and mixed by pipetting. 100ul aliquots were taken out for DNA and RNA extraction from the same sample. RNA extraction was done using Qiagen RNeasy mini kit (Qiagen, Hilden, Germany) with on-column DNase digestion. Final elution was made in 30 μL dH2O. The concentration and integrity of the total RNA was estimated by Quant-iT™ RiboGreen® RNA Assay Kit  (ThermoFisher Scientific, Waltham, MA), and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA), respectively. PGCGROWTHCONDITIONS
Genome_build: Escherichia coli (DH10B) PGCGROWTHCONDITIONS
gentamycin concentration (ug/ml): 75 PGCGROWTHCONDITIONS
location: Earth PGCGROWTHCONDITIONS
Nineteen hours after experiment start, antibiotic (Gentamicin Sulfate (MP Biomedical, Cat No. 1676045, Santa Ana, CA, USA)) was introducing into the cultures. Antibiotic concentration varied from one sample to the next from 0 to 150 ug/mL in 25 ug/mL steps. Thirty hours later, samples were fixed in RNA Later II ((ACROS, Cat. No. 41678, New Jersey, USA)). Samples were stored at -75C until return to Earth for analyses. PGCGROWTHCONDITIONS
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Data-analysis was performed using the CLC Genomics Workbench (Version 7.5.1, CLC Bio, Aarhus, Denmark). The reference genome Escherichia coli (DH10B) sequence was downloaded from the UCSC genome browser. For read mapping, the following parameters were used: mismatch cost = 2, insertion and deletion cost = 3, length fraction: 0.8, similarity fraction = 0.8, global alignment = no, auto-detect paired distances = yes. Samples were grouped and differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions. PGCGROWTHCONDITIONS
Ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold (Yeast) kit (Epicenter, Madison, WI) using manufacturer's recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and adapter ligation. Post-ligated materials were individually barcoded with primers and amplified through 12 cycles of PCR. Final library quantity was assessed by Quant-iT™ PicoGreen® dsDNA Assay Kit and the library quality was estimated on LabChip® GX (Caliper, PerkinElmer, Waltham, MA). Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5 nM and pooled equimolar prior to clustering. Paired-End (PE) sequencing was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc.). PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were sent to the International Space Station at 4C in FPAs, as described above. Temperature was increased to 37C and 23 hours later, the experiment was started by introducing the inoculum (E. coli ATCC 4157) into the growth medium (Medium E as described in Vogel & Bonner (1956) supplemented with 5 g/L glucose), yielding 3.25 mL of a culture with a starting cell concentration of 1.22e6 cell/mL. PGCGROWTHCONDITIONS
strain: ATCC 4157 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: excel file include RPKM values for each Sample PGCGROWTHCONDITIONS
CAR005 strain PGCGROWTHCONDITIONS
CAR005 PGCGROWTHCONDITIONS
Detailed parameters for reads mapping: bowtie2 -x ATCC8739 -1 X_1.fq -2 X_2.fq --no-mixed -p 2 -S X.sam PGCGROWTHCONDITIONS
Escherichia coli ATCC 8739 PGCGROWTHCONDITIONS
Genome_build: ASM1938v1 PGCGROWTHCONDITIONS
Illumina Casava1.7 software used for basecalling. PGCGROWTHCONDITIONS
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli ATCC8739 genome (GenBank CP000946.1) using Bowtie 2 (version 2.2.5) PGCGROWTHCONDITIONS
Single colonies were inoculated into 15x100 mm tubes containing 4 ml LB, and grown at 30ºC and 250 rpm overnight. 100 μl seed culture was inoculated into a 100 ml flask containing 10 ml LB medium, and grown at 30ºC and 250 rpm for 5 h. PGCGROWTHCONDITIONS
strain: CAR005 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: [.txt] tab-delimited text file includes RPKM values PGCGROWTHCONDITIONS
Total RNA was isolated by the Trizol-Phenol-Chloroform method. An additional clean-up including the on-column DNase I treatment was performed by using the RNeasy mini kit (Qiagen). PGCGROWTHCONDITIONS
Detailed parameters for reads mapping: bowtie2 -x ATCC8739 -1 X_1.fq -2 X_2.fq --no-mixed -p 2 -S X.sam PGCGROWTHCONDITIONS
Escherichia coli ATCC 8739 PGCGROWTHCONDITIONS
G4H14 strain PGCGROWTHCONDITIONS
G4H14 PGCGROWTHCONDITIONS
Genome_build: ASM1938v1 PGCGROWTHCONDITIONS
Illumina Casava1.7 software used for basecalling. PGCGROWTHCONDITIONS
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli ATCC8739 genome (GenBank CP000946.1) using Bowtie 2 (version 2.2.5) PGCGROWTHCONDITIONS
Single colonies were inoculated into 15x100 mm tubes containing 4 ml LB, and grown at 30ºC and 250 rpm overnight. 100 μl seed culture was inoculated into a 100 ml flask containing 10 ml LB medium, and grown at 30ºC and 250 rpm for 5 h. PGCGROWTHCONDITIONS
strain: G4H14 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: [.txt] tab-delimited text file includes RPKM values PGCGROWTHCONDITIONS
Total RNA was isolated by the Trizol-Phenol-Chloroform method. An additional clean-up including the on-column DNase I treatment was performed by using the RNeasy mini kit (Qiagen). PGCGROWTHCONDITIONS
Detailed parameters for reads mapping: bowtie2 -x ATCC8739 -1 X_1.fq -2 X_2.fq --no-mixed -p 2 -S X.sam PGCGROWTHCONDITIONS
Escherichia coli ATCC 8739 PGCGROWTHCONDITIONS
Genome_build: ASM1938v1 PGCGROWTHCONDITIONS
Illumina Casava1.7 software used for basecalling. PGCGROWTHCONDITIONS
IspG1 strain PGCGROWTHCONDITIONS
IspG1 PGCGROWTHCONDITIONS
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli ATCC8739 genome (GenBank CP000946.1) using Bowtie 2 (version 2.2.5) PGCGROWTHCONDITIONS
Single colonies were inoculated into 15x100 mm tubes containing 4 ml LB, and grown at 30ºC and 250 rpm overnight. 100 μl seed culture was inoculated into a 100 ml flask containing 10 ml LB medium, and grown at 30ºC and 250 rpm for 5 h. PGCGROWTHCONDITIONS
strain: IspG1 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: [.txt] tab-delimited text file includes RPKM values PGCGROWTHCONDITIONS
Total RNA was isolated by the Trizol-Phenol-Chloroform method. An additional clean-up including the on-column DNase I treatment was performed by using the RNeasy mini kit (Qiagen). PGCGROWTHCONDITIONS
Detailed parameters for reads mapping: bowtie2 -x ATCC8739 -1 X_1.fq -2 X_2.fq --no-mixed -p 2 -S X.sam PGCGROWTHCONDITIONS
E.coli cells PGCGROWTHCONDITIONS
Escherichia coli ATCC 8739 PGCGROWTHCONDITIONS
Genome_build: ATCC8739 PGCGROWTHCONDITIONS
growth condition: normal condtion (5% w/v glucose) PGCGROWTHCONDITIONS
Illumina Casava1.7 software used for basecalling. PGCGROWTHCONDITIONS
NZ502_5%Glu PGCGROWTHCONDITIONS
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli ATCC8739 genome (GenBank CP000946.1) using Bowtie 2 (version 2.2.5) PGCGROWTHCONDITIONS
strain: NZ-502 (RpoB mutant) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample . PGCGROWTHCONDITIONS
Total RNA was isolated by the Trizol-Phenol-Chloroform method. An additional clean-up including the on-column DNase I treatment was performed by using the RNeasy mini kit (Qiagen). PGCGROWTHCONDITIONS
Detailed parameters for reads mapping: bowtie2 -x ATCC8739 -1 X_1.fq -2 X_2.fq --no-mixed -p 2 -S X.sam PGCGROWTHCONDITIONS
E.coli cells PGCGROWTHCONDITIONS
Escherichia coli ATCC 8739 PGCGROWTHCONDITIONS
Genome_build: ATCC8739 PGCGROWTHCONDITIONS
growth condition: osmotic stress condtion (12% w/v glucose) PGCGROWTHCONDITIONS
Illumina Casava1.7 software used for basecalling. PGCGROWTHCONDITIONS
NZ502_12%Glu PGCGROWTHCONDITIONS
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli ATCC8739 genome (GenBank CP000946.1) using Bowtie 2 (version 2.2.5) PGCGROWTHCONDITIONS
strain: NZ-502 (RpoB mutant) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample . PGCGROWTHCONDITIONS
Total RNA was isolated by the Trizol-Phenol-Chloroform method. An additional clean-up including the on-column DNase I treatment was performed by using the RNeasy mini kit (Qiagen). PGCGROWTHCONDITIONS
Detailed parameters for reads mapping: bowtie2 -x ATCC8739 -1 X_1.fq -2 X_2.fq --no-mixed -p 2 -S X.sam PGCGROWTHCONDITIONS
E.coli cells PGCGROWTHCONDITIONS
Escherichia coli ATCC 8739 PGCGROWTHCONDITIONS
Genome_build: ATCC8739 PGCGROWTHCONDITIONS
growth condition: normal condtion (5% w/v glucose) PGCGROWTHCONDITIONS
Illumina Casava1.7 software used for basecalling. PGCGROWTHCONDITIONS
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli ATCC8739 genome (GenBank CP000946.1) using Bowtie 2 (version 2.2.5) PGCGROWTHCONDITIONS
strain: Suc-T110 (parental strain) PGCGROWTHCONDITIONS
SucT110_5%Glu PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample . PGCGROWTHCONDITIONS
Total RNA was isolated by the Trizol-Phenol-Chloroform method. An additional clean-up including the on-column DNase I treatment was performed by using the RNeasy mini kit (Qiagen). PGCGROWTHCONDITIONS
Detailed parameters for reads mapping: bowtie2 -x ATCC8739 -1 X_1.fq -2 X_2.fq --no-mixed -p 2 -S X.sam PGCGROWTHCONDITIONS
E.coli cells PGCGROWTHCONDITIONS
Escherichia coli ATCC 8739 PGCGROWTHCONDITIONS
Genome_build: ATCC8739 PGCGROWTHCONDITIONS
growth condition: osmotic stress condtion (12% w/v glucose) PGCGROWTHCONDITIONS
Illumina Casava1.7 software used for basecalling. PGCGROWTHCONDITIONS
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli ATCC8739 genome (GenBank CP000946.1) using Bowtie 2 (version 2.2.5) PGCGROWTHCONDITIONS
strain: Suc-T110 (parental strain) PGCGROWTHCONDITIONS
SucT110_12%Glu PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample . PGCGROWTHCONDITIONS
Total RNA was isolated by the Trizol-Phenol-Chloroform method. An additional clean-up including the on-column DNase I treatment was performed by using the RNeasy mini kit (Qiagen). PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
WT- Keio Sample 1 PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
∆zwf parent Sample 2 PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
zwf suppressor 1-1 Sample 3 PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
zwf suppressor 1-2 Sample 4 PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
∆ppk parent Sample 5 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
ppk suppressor 1-1 Sample 6 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
ppk suppressor 2-1 Sample 7 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
ppk suppressor 3-1 Sample 8 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
∆dapF parent Sample 9 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
dapF suppressor 1-1 Sample 10 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
dapF suppressor 3-1 Sample 11 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
∆entC parent Sample 12 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
entC suppressor 1-1 Sample 13 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
entC suppressor 2-1 Sample 14 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
entC suppressor 3-1 Sample 15 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
∆dgk parent Sample 16 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
dgk suppressor 1-1 Sample 17 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
dgk suppressor 2-1 Sample 18 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
dgk suppressor 3-1 Sample 19 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
WT- Keio Sample 20 PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
∆zwf parent Sample 21 PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
zwf suppressor 1-1 Sample 22 PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
zwf suppressor 1-2 Sample 23 PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
∆ppk parent Sample 24 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
ppk suppressor 1-1 Sample 25 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
ppk suppressor 2-1 Sample 26 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
ppk suppressor 3-1 Sample 27 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
∆dapF parent Sample 28 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
dapF suppressor 1-1 Sample 29 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
dapF suppressor 3-1 Sample 30 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
∆entC parent Sample 31 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
entC suppressor 1-1 Sample 32 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
entC suppressor 2-1 Sample 33 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
entC suppressor 3-1 Sample 34 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
∆dgk parent Sample 35 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
dgk suppressor 1-1 Sample 36 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
dgk suppressor 2-1 Sample 37 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
dgk suppressor 3-1 Sample 38 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
WT- Keio Sample 39 PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
∆zwf parent Sample 40 PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
zwf suppressor 1-1 Sample 41 PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
zwf suppressor 1-2 Sample 42 PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
∆ppk parent Sample 43 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
ppk suppressor 1-1 Sample 44 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
ppk suppressor 2-1 Sample 45 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
ppk suppressor 3-1 Sample 46 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
∆dapF parent Sample 47 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
dapF suppressor 1-1 Sample 48 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
dapF suppressor 3-1 Sample 49 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
∆entC parent Sample 50 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
entC suppressor 1-1 Sample 51 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
entC suppressor 2-1 Sample 52 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
entC suppressor 3-1 Sample 53 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
∆dgk parent Sample 54 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
dgk suppressor 1-1 Sample 55 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
dgk suppressor 2-1 Sample 56 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
base calls with quality metrics were generated using the HiSeq 2500 Control software PGCGROWTHCONDITIONS
cells were grown in M9 glucose (0.4% w/v) PGCGROWTHCONDITIONS
dgk suppressor 3-1 Sample 57 PGCGROWTHCONDITIONS
Escherichia coli cell lysate PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: E. coli strain BW25113 PGCGROWTHCONDITIONS
library construction followed Illumina manufacturer protocol for bacteria using the Nextera XT DNA Library Preparation Kit PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using standard Trizol lysis and aqueous extraction, followed by further purification using a Qiagen RNAeasy kit. PGCGROWTHCONDITIONS
sequences were aligned to the parent E. coli strain genome template and transcript levels were quantified for triplicate groups of each primary deletion strain and synthetic rescue (i.e. sup) strain using Rockhopper (version 2.0.3) PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
transcript abundance was quantified using rockhopper PGCGROWTHCONDITIONS
10J.0 PGCGROWTHCONDITIONS
200 bp insert, rRNA depletion PGCGROWTHCONDITIONS
biological replicate: t=0 Replicate 1 PGCGROWTHCONDITIONS
E. coli were sampled at times = 0, 1 hour, and 2 hours following release from stationary phase. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli MG1655 reference genome (NC_00091313-Feb-2011 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA sequences were quality assessed and trimmed using FastQC version 0.10.1 (www.bioinformatics.babraham.ac.uk/projects/fastqc/). The identification of differentially expressed genes was performed using cufflinks version 2.0.2 to analyse the trimmed sequences as a time course. Briefly, trimmed reads were aligned to the E. coli MG1655 reference genome (NC_000913 13-Feb-2011) using Tophat version 2.0.7. Aligned reads were assembled for differential expression using cufflinks version and merged using cuffmerge with an ‘assemblies’ file containing the transcript.gtf output files from culfflinks. Differential expression analysis was performed using the merged.gtf output file from cuffmerge. PGCGROWTHCONDITIONS
RNA was extracted from two biological replicates (30 mL) of each bacterial culture isolated at each time point. The 30 mL culture was aliquoted into three 15 mL tubes containing 5 mL of ice-cold EtOH/Phenol stop solution (5% water-saturated phenol pH 4.2 [Invitrogen] in 100% ethanol). Cells were collected by centrifugation (4,000 rpm, 5 min, 4°C) and the pellet suspended in 800 µL TE pH 8.0 supplemented with 0.5 mg/mL lysozyme. SDS (80 µL at 10% (w/v)) was added, samples mixed by inversion, and incubated (65°C, 2 min), before the addition of 88 µL 1 M NaOAc (pH 5.2). Each sample was added to an equal volume (1mL) of water-saturated phenol (pH 4.2, 65°C) and incubated (65°C, 6 min). The solution was separated into layers by centrifugation (14,000 rpm, 10 min, 4°C) and the upper aqueous RNA containing layer removed and transferred into a fresh tube.  RNA was cleaned by three extractions with phenol:CHCl3:IAA (25:24:1, pH 8.0) before being precipitated (-80°C, O/N) following the addition of 1/10 volume of 3M NaOAc (pH 5.2) and 2 volumes of ice cold 100% EtOH. RNA was pelleted (14,000 rpm, 25 min, 4°C), the supernatant removed and the pellet washed with 1 mL 75% cold EtOH (made with DEPC-treated water). PGCGROWTHCONDITIONS
RNA was extracted from two biological replicates (30 mL) of each bacterial culture isolated at each time point. The 30 mL culture was aliquoted into three 15 mL tubes containing 5 mL of ice-cold EtOH/Phenol stop solution (5% water-saturated phenol pH 4.2 [Invitrogen] in 100% ethanol). Cells were collected by centrifugation (4,000 rpm, 5 min, 4°C) and the pellet suspended in 800 µL TE pH 8.0 supplemented with 0.5 mg/mL lysozyme. SDS (80 µL at 10% (w/v)) was added, samples mixed by inversion, and incubated (65°C, 2 min), before the addition of 88 µL 1 M NaOAc (pH 5.2). Each sample was added to an equal volume (1mL) of water-saturated phenol (pH 4.2, 65°C) and incubated (65°C, 6 min). The solution was separated into layers by centrifugation (14,000 rpm, 10 min, 4°C) and the upper aqueous RNA containing layer removed and transferred into a fresh tube.  RNA was cleaned by three extractions with phenol:CHCl3:IAA (25:24:1, pH 8.0) before being precipitated (-80°C, O/N) following the addition of 1/10 volume of 3M NaOAc (pH 5.2) and 2 volumes of ice cold 100% EtOH. RNA was pelleted (14,000 rpm, 25 min, 4°C), the supernatant removed and the pellet washed with 1 mL 75% cold EtOH (made with DEPC-treated water).   RNA was pelleted (14,000 rpm, 5 min, 4°C) and air dried before suspension in 80 µL RNAse free water (Invitrogen) and treatment with TURBO DNAse (Ambion) according to the manufacturer’s instructions. Briefly, 0.1 V of 10 X Turbo DNAse buffer (Ambion) was added to the RNA solution. 1 µL of TURBO DNAse was added to the solution, which was then incubated (30 min, 37 °C). Following incubation, 0.1 V of DNase Inactivation Reagent (Ambion) was added and then incubated (5 min, RT) with occasional mixing. RNA was isolated and transferred into a fresh microfuge tube.  RNA quality tested using the the Agilent RNA 6000 Nano Kit (Agilent Technologies) and quality analysed using the Agilent 2100 Bioanalyzer (Agilent Technologies). PGCGROWTHCONDITIONS
RNA was pelleted (14,000 rpm, 5 min, 4°C) and air dried before suspension in 80 µL RNAse free water (Invitrogen) and treatment with TURBO DNAse (Ambion) according to the manufacturer’s instructions. Briefly, 0.1 V of 10 X Turbo DNAse buffer (Ambion) was added to the RNA solution. 1 µL of TURBO DNAse was added to the solution, which was then incubated (30 min, 37 °C). Following incubation, 0.1 V of DNase Inactivation Reagent (Ambion) was added and then incubated (5 min, RT) with occasional mixing. RNA was isolated and transferred into a fresh microfuge tube.  RNA quality tested using the the Agilent RNA 6000 Nano Kit (Agilent Technologies) and quality analysed using the Agilent 2100 Bioanalyzer (Agilent Technologies). PGCGROWTHCONDITIONS
Stationary phase  t=0 PGCGROWTHCONDITIONS
Synchronization was achieved by passaging cells through one or two rounds of stationary phase according to Cutler and Evans 1966. Briefly: Individual colonies (LB plate, 37°C, 24 h) were inoculated into M9 media and grown O/N (37°C, 200 rpm). M9 media was inoculated to a final OD600 = 0.25 (early-logarithmic phase). Cultures were grown (37°C, 200 rpm) and maintained in stationary phase (OD600 1.8) for approximately 2 hours. An appropriate amount of each culture was used to inoculate pre-warmed (37°C) M9 media to a final OD600 = 0.25 (approximate 7-fold dilution). Released cultures were grown (37°C, 200 rpm) and harvested (time = 0, 1 hr, or 2 hr) for GCC and RNA isolation. Samples (1 mL) were also taken for FACS analysis and fluorescence microscopy (t=0, 1 hr, and 2 hr). PGCGROWTHCONDITIONS
time post release: E. coli cells immediately following release from Stationary phase  t=0 PGCGROWTHCONDITIONS
11K.60 PGCGROWTHCONDITIONS
200 bp insert, rRNA depletion PGCGROWTHCONDITIONS
biological replicate: Replicate 1 PGCGROWTHCONDITIONS
E. coli were sampled at times = 0, 1 hour, and 2 hours following release from stationary phase. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli MG1655 reference genome (NC_00091313-Feb-2011 PGCGROWTHCONDITIONS
Growing  t=1 hour PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA sequences were quality assessed and trimmed using FastQC version 0.10.1 (www.bioinformatics.babraham.ac.uk/projects/fastqc/). The identification of differentially expressed genes was performed using cufflinks version 2.0.2 to analyse the trimmed sequences as a time course. Briefly, trimmed reads were aligned to the E. coli MG1655 reference genome (NC_000913 13-Feb-2011) using Tophat version 2.0.7. Aligned reads were assembled for differential expression using cufflinks version and merged using cuffmerge with an ‘assemblies’ file containing the transcript.gtf output files from culfflinks. Differential expression analysis was performed using the merged.gtf output file from cuffmerge. PGCGROWTHCONDITIONS
RNA was extracted from two biological replicates (30 mL) of each bacterial culture isolated at each time point. The 30 mL culture was aliquoted into three 15 mL tubes containing 5 mL of ice-cold EtOH/Phenol stop solution (5% water-saturated phenol pH 4.2 [Invitrogen] in 100% ethanol). Cells were collected by centrifugation (4,000 rpm, 5 min, 4°C) and the pellet suspended in 800 µL TE pH 8.0 supplemented with 0.5 mg/mL lysozyme. SDS (80 µL at 10% (w/v)) was added, samples mixed by inversion, and incubated (65°C, 2 min), before the addition of 88 µL 1 M NaOAc (pH 5.2). Each sample was added to an equal volume (1mL) of water-saturated phenol (pH 4.2, 65°C) and incubated (65°C, 6 min). The solution was separated into layers by centrifugation (14,000 rpm, 10 min, 4°C) and the upper aqueous RNA containing layer removed and transferred into a fresh tube.  RNA was cleaned by three extractions with phenol:CHCl3:IAA (25:24:1, pH 8.0) before being precipitated (-80°C, O/N) following the addition of 1/10 volume of 3M NaOAc (pH 5.2) and 2 volumes of ice cold 100% EtOH. RNA was pelleted (14,000 rpm, 25 min, 4°C), the supernatant removed and the pellet washed with 1 mL 75% cold EtOH (made with DEPC-treated water). PGCGROWTHCONDITIONS
RNA was extracted from two biological replicates (30 mL) of each bacterial culture isolated at each time point. The 30 mL culture was aliquoted into three 15 mL tubes containing 5 mL of ice-cold EtOH/Phenol stop solution (5% water-saturated phenol pH 4.2 [Invitrogen] in 100% ethanol). Cells were collected by centrifugation (4,000 rpm, 5 min, 4°C) and the pellet suspended in 800 µL TE pH 8.0 supplemented with 0.5 mg/mL lysozyme. SDS (80 µL at 10% (w/v)) was added, samples mixed by inversion, and incubated (65°C, 2 min), before the addition of 88 µL 1 M NaOAc (pH 5.2). Each sample was added to an equal volume (1mL) of water-saturated phenol (pH 4.2, 65°C) and incubated (65°C, 6 min). The solution was separated into layers by centrifugation (14,000 rpm, 10 min, 4°C) and the upper aqueous RNA containing layer removed and transferred into a fresh tube.  RNA was cleaned by three extractions with phenol:CHCl3:IAA (25:24:1, pH 8.0) before being precipitated (-80°C, O/N) following the addition of 1/10 volume of 3M NaOAc (pH 5.2) and 2 volumes of ice cold 100% EtOH. RNA was pelleted (14,000 rpm, 25 min, 4°C), the supernatant removed and the pellet washed with 1 mL 75% cold EtOH (made with DEPC-treated water).   RNA was pelleted (14,000 rpm, 5 min, 4°C) and air dried before suspension in 80 µL RNAse free water (Invitrogen) and treatment with TURBO DNAse (Ambion) according to the manufacturer’s instructions. Briefly, 0.1 V of 10 X Turbo DNAse buffer (Ambion) was added to the RNA solution. 1 µL of TURBO DNAse was added to the solution, which was then incubated (30 min, 37 °C). Following incubation, 0.1 V of DNase Inactivation Reagent (Ambion) was added and then incubated (5 min, RT) with occasional mixing. RNA was isolated and transferred into a fresh microfuge tube.  RNA quality tested using the the Agilent RNA 6000 Nano Kit (Agilent Technologies) and quality analysed using the Agilent 2100 Bioanalyzer (Agilent Technologies). PGCGROWTHCONDITIONS
RNA was pelleted (14,000 rpm, 5 min, 4°C) and air dried before suspension in 80 µL RNAse free water (Invitrogen) and treatment with TURBO DNAse (Ambion) according to the manufacturer’s instructions. Briefly, 0.1 V of 10 X Turbo DNAse buffer (Ambion) was added to the RNA solution. 1 µL of TURBO DNAse was added to the solution, which was then incubated (30 min, 37 °C). Following incubation, 0.1 V of DNase Inactivation Reagent (Ambion) was added and then incubated (5 min, RT) with occasional mixing. RNA was isolated and transferred into a fresh microfuge tube.  RNA quality tested using the the Agilent RNA 6000 Nano Kit (Agilent Technologies) and quality analysed using the Agilent 2100 Bioanalyzer (Agilent Technologies). PGCGROWTHCONDITIONS
Synchronization was achieved by passaging cells through one or two rounds of stationary phase according to Cutler and Evans 1966. Briefly: Individual colonies (LB plate, 37°C, 24 h) were inoculated into M9 media and grown O/N (37°C, 200 rpm). M9 media was inoculated to a final OD600 = 0.25 (early-logarithmic phase). Cultures were grown (37°C, 200 rpm) and maintained in stationary phase (OD600 1.8) for approximately 2 hours. An appropriate amount of each culture was used to inoculate pre-warmed (37°C) M9 media to a final OD600 = 0.25 (approximate 7-fold dilution). Released cultures were grown (37°C, 200 rpm) and harvested (time = 0, 1 hr, or 2 hr) for GCC and RNA isolation. Samples (1 mL) were also taken for FACS analysis and fluorescence microscopy (t=0, 1 hr, and 2 hr). PGCGROWTHCONDITIONS
time post release: E. coli cells 1 hour following release from Stationary phase  (t=1) PGCGROWTHCONDITIONS
12L.120 PGCGROWTHCONDITIONS
200 bp insert, rRNA depletion PGCGROWTHCONDITIONS
biological replicate: Replicate 1 PGCGROWTHCONDITIONS
Dividing t=2 hours PGCGROWTHCONDITIONS
E. coli were sampled at times = 0, 1 hour, and 2 hours following release from stationary phase. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli MG1655 reference genome (NC_00091313-Feb-2011 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA sequences were quality assessed and trimmed using FastQC version 0.10.1 (www.bioinformatics.babraham.ac.uk/projects/fastqc/). The identification of differentially expressed genes was performed using cufflinks version 2.0.2 to analyse the trimmed sequences as a time course. Briefly, trimmed reads were aligned to the E. coli MG1655 reference genome (NC_000913 13-Feb-2011) using Tophat version 2.0.7. Aligned reads were assembled for differential expression using cufflinks version and merged using cuffmerge with an ‘assemblies’ file containing the transcript.gtf output files from culfflinks. Differential expression analysis was performed using the merged.gtf output file from cuffmerge. PGCGROWTHCONDITIONS
RNA was extracted from two biological replicates (30 mL) of each bacterial culture isolated at each time point. The 30 mL culture was aliquoted into three 15 mL tubes containing 5 mL of ice-cold EtOH/Phenol stop solution (5% water-saturated phenol pH 4.2 [Invitrogen] in 100% ethanol). Cells were collected by centrifugation (4,000 rpm, 5 min, 4°C) and the pellet suspended in 800 µL TE pH 8.0 supplemented with 0.5 mg/mL lysozyme. SDS (80 µL at 10% (w/v)) was added, samples mixed by inversion, and incubated (65°C, 2 min), before the addition of 88 µL 1 M NaOAc (pH 5.2). Each sample was added to an equal volume (1mL) of water-saturated phenol (pH 4.2, 65°C) and incubated (65°C, 6 min). The solution was separated into layers by centrifugation (14,000 rpm, 10 min, 4°C) and the upper aqueous RNA containing layer removed and transferred into a fresh tube.  RNA was cleaned by three extractions with phenol:CHCl3:IAA (25:24:1, pH 8.0) before being precipitated (-80°C, O/N) following the addition of 1/10 volume of 3M NaOAc (pH 5.2) and 2 volumes of ice cold 100% EtOH. RNA was pelleted (14,000 rpm, 25 min, 4°C), the supernatant removed and the pellet washed with 1 mL 75% cold EtOH (made with DEPC-treated water). PGCGROWTHCONDITIONS
RNA was extracted from two biological replicates (30 mL) of each bacterial culture isolated at each time point. The 30 mL culture was aliquoted into three 15 mL tubes containing 5 mL of ice-cold EtOH/Phenol stop solution (5% water-saturated phenol pH 4.2 [Invitrogen] in 100% ethanol). Cells were collected by centrifugation (4,000 rpm, 5 min, 4°C) and the pellet suspended in 800 µL TE pH 8.0 supplemented with 0.5 mg/mL lysozyme. SDS (80 µL at 10% (w/v)) was added, samples mixed by inversion, and incubated (65°C, 2 min), before the addition of 88 µL 1 M NaOAc (pH 5.2). Each sample was added to an equal volume (1mL) of water-saturated phenol (pH 4.2, 65°C) and incubated (65°C, 6 min). The solution was separated into layers by centrifugation (14,000 rpm, 10 min, 4°C) and the upper aqueous RNA containing layer removed and transferred into a fresh tube.  RNA was cleaned by three extractions with phenol:CHCl3:IAA (25:24:1, pH 8.0) before being precipitated (-80°C, O/N) following the addition of 1/10 volume of 3M NaOAc (pH 5.2) and 2 volumes of ice cold 100% EtOH. RNA was pelleted (14,000 rpm, 25 min, 4°C), the supernatant removed and the pellet washed with 1 mL 75% cold EtOH (made with DEPC-treated water).   RNA was pelleted (14,000 rpm, 5 min, 4°C) and air dried before suspension in 80 µL RNAse free water (Invitrogen) and treatment with TURBO DNAse (Ambion) according to the manufacturer’s instructions. Briefly, 0.1 V of 10 X Turbo DNAse buffer (Ambion) was added to the RNA solution. 1 µL of TURBO DNAse was added to the solution, which was then incubated (30 min, 37 °C). Following incubation, 0.1 V of DNase Inactivation Reagent (Ambion) was added and then incubated (5 min, RT) with occasional mixing. RNA was isolated and transferred into a fresh microfuge tube.  RNA quality tested using the the Agilent RNA 6000 Nano Kit (Agilent Technologies) and quality analysed using the Agilent 2100 Bioanalyzer (Agilent Technologies). PGCGROWTHCONDITIONS
RNA was pelleted (14,000 rpm, 5 min, 4°C) and air dried before suspension in 80 µL RNAse free water (Invitrogen) and treatment with TURBO DNAse (Ambion) according to the manufacturer’s instructions. Briefly, 0.1 V of 10 X Turbo DNAse buffer (Ambion) was added to the RNA solution. 1 µL of TURBO DNAse was added to the solution, which was then incubated (30 min, 37 °C). Following incubation, 0.1 V of DNase Inactivation Reagent (Ambion) was added and then incubated (5 min, RT) with occasional mixing. RNA was isolated and transferred into a fresh microfuge tube.  RNA quality tested using the the Agilent RNA 6000 Nano Kit (Agilent Technologies) and quality analysed using the Agilent 2100 Bioanalyzer (Agilent Technologies). PGCGROWTHCONDITIONS
Synchronization was achieved by passaging cells through one or two rounds of stationary phase according to Cutler and Evans 1966. Briefly: Individual colonies (LB plate, 37°C, 24 h) were inoculated into M9 media and grown O/N (37°C, 200 rpm). M9 media was inoculated to a final OD600 = 0.25 (early-logarithmic phase). Cultures were grown (37°C, 200 rpm) and maintained in stationary phase (OD600 1.8) for approximately 2 hours. An appropriate amount of each culture was used to inoculate pre-warmed (37°C) M9 media to a final OD600 = 0.25 (approximate 7-fold dilution). Released cultures were grown (37°C, 200 rpm) and harvested (time = 0, 1 hr, or 2 hr) for GCC and RNA isolation. Samples (1 mL) were also taken for FACS analysis and fluorescence microscopy (t=0, 1 hr, and 2 hr). PGCGROWTHCONDITIONS
time post release: E. coli cells 2 hour2 following release from Stationary phase  (t=2) PGCGROWTHCONDITIONS
200 bp insert, rRNA depletion PGCGROWTHCONDITIONS
7G.0 PGCGROWTHCONDITIONS
biological replicate: t=0 replicate 2 PGCGROWTHCONDITIONS
E. coli were sampled at times = 0, 1 hour, and 2 hours following release from stationary phase. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli MG1655 reference genome (NC_00091313-Feb-2011 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA sequences were quality assessed and trimmed using FastQC version 0.10.1 (www.bioinformatics.babraham.ac.uk/projects/fastqc/). The identification of differentially expressed genes was performed using cufflinks version 2.0.2 to analyse the trimmed sequences as a time course. Briefly, trimmed reads were aligned to the E. coli MG1655 reference genome (NC_000913 13-Feb-2011) using Tophat version 2.0.7. Aligned reads were assembled for differential expression using cufflinks version and merged using cuffmerge with an ‘assemblies’ file containing the transcript.gtf output files from culfflinks. Differential expression analysis was performed using the merged.gtf output file from cuffmerge. PGCGROWTHCONDITIONS
RNA was extracted from two biological replicates (30 mL) of each bacterial culture isolated at each time point. The 30 mL culture was aliquoted into three 15 mL tubes containing 5 mL of ice-cold EtOH/Phenol stop solution (5% water-saturated phenol pH 4.2 [Invitrogen] in 100% ethanol). Cells were collected by centrifugation (4,000 rpm, 5 min, 4°C) and the pellet suspended in 800 µL TE pH 8.0 supplemented with 0.5 mg/mL lysozyme. SDS (80 µL at 10% (w/v)) was added, samples mixed by inversion, and incubated (65°C, 2 min), before the addition of 88 µL 1 M NaOAc (pH 5.2). Each sample was added to an equal volume (1mL) of water-saturated phenol (pH 4.2, 65°C) and incubated (65°C, 6 min). The solution was separated into layers by centrifugation (14,000 rpm, 10 min, 4°C) and the upper aqueous RNA containing layer removed and transferred into a fresh tube.  RNA was cleaned by three extractions with phenol:CHCl3:IAA (25:24:1, pH 8.0) before being precipitated (-80°C, O/N) following the addition of 1/10 volume of 3M NaOAc (pH 5.2) and 2 volumes of ice cold 100% EtOH. RNA was pelleted (14,000 rpm, 25 min, 4°C), the supernatant removed and the pellet washed with 1 mL 75% cold EtOH (made with DEPC-treated water). PGCGROWTHCONDITIONS
RNA was extracted from two biological replicates (30 mL) of each bacterial culture isolated at each time point. The 30 mL culture was aliquoted into three 15 mL tubes containing 5 mL of ice-cold EtOH/Phenol stop solution (5% water-saturated phenol pH 4.2 [Invitrogen] in 100% ethanol). Cells were collected by centrifugation (4,000 rpm, 5 min, 4°C) and the pellet suspended in 800 µL TE pH 8.0 supplemented with 0.5 mg/mL lysozyme. SDS (80 µL at 10% (w/v)) was added, samples mixed by inversion, and incubated (65°C, 2 min), before the addition of 88 µL 1 M NaOAc (pH 5.2). Each sample was added to an equal volume (1mL) of water-saturated phenol (pH 4.2, 65°C) and incubated (65°C, 6 min). The solution was separated into layers by centrifugation (14,000 rpm, 10 min, 4°C) and the upper aqueous RNA containing layer removed and transferred into a fresh tube.  RNA was cleaned by three extractions with phenol:CHCl3:IAA (25:24:1, pH 8.0) before being precipitated (-80°C, O/N) following the addition of 1/10 volume of 3M NaOAc (pH 5.2) and 2 volumes of ice cold 100% EtOH. RNA was pelleted (14,000 rpm, 25 min, 4°C), the supernatant removed and the pellet washed with 1 mL 75% cold EtOH (made with DEPC-treated water).   RNA was pelleted (14,000 rpm, 5 min, 4°C) and air dried before suspension in 80 µL RNAse free water (Invitrogen) and treatment with TURBO DNAse (Ambion) according to the manufacturer’s instructions. Briefly, 0.1 V of 10 X Turbo DNAse buffer (Ambion) was added to the RNA solution. 1 µL of TURBO DNAse was added to the solution, which was then incubated (30 min, 37 °C). Following incubation, 0.1 V of DNase Inactivation Reagent (Ambion) was added and then incubated (5 min, RT) with occasional mixing. RNA was isolated and transferred into a fresh microfuge tube.  RNA quality tested using the the Agilent RNA 6000 Nano Kit (Agilent Technologies) and quality analysed using the Agilent 2100 Bioanalyzer (Agilent Technologies). PGCGROWTHCONDITIONS
RNA was pelleted (14,000 rpm, 5 min, 4°C) and air dried before suspension in 80 µL RNAse free water (Invitrogen) and treatment with TURBO DNAse (Ambion) according to the manufacturer’s instructions. Briefly, 0.1 V of 10 X Turbo DNAse buffer (Ambion) was added to the RNA solution. 1 µL of TURBO DNAse was added to the solution, which was then incubated (30 min, 37 °C). Following incubation, 0.1 V of DNase Inactivation Reagent (Ambion) was added and then incubated (5 min, RT) with occasional mixing. RNA was isolated and transferred into a fresh microfuge tube.  RNA quality tested using the the Agilent RNA 6000 Nano Kit (Agilent Technologies) and quality analysed using the Agilent 2100 Bioanalyzer (Agilent Technologies). PGCGROWTHCONDITIONS
Stationary phase  t=0 PGCGROWTHCONDITIONS
Synchronization was achieved by passaging cells through one or two rounds of stationary phase according to Cutler and Evans 1966. Briefly: Individual colonies (LB plate, 37°C, 24 h) were inoculated into M9 media and grown O/N (37°C, 200 rpm). M9 media was inoculated to a final OD600 = 0.25 (early-logarithmic phase). Cultures were grown (37°C, 200 rpm) and maintained in stationary phase (OD600 1.8) for approximately 2 hours. An appropriate amount of each culture was used to inoculate pre-warmed (37°C) M9 media to a final OD600 = 0.25 (approximate 7-fold dilution). Released cultures were grown (37°C, 200 rpm) and harvested (time = 0, 1 hr, or 2 hr) for GCC and RNA isolation. Samples (1 mL) were also taken for FACS analysis and fluorescence microscopy (t=0, 1 hr, and 2 hr). PGCGROWTHCONDITIONS
time post release: E. coli cells immediately following release from Stationary phase  t=0 PGCGROWTHCONDITIONS
100% rep1 PGCGROWTHCONDITIONS
Base calls performed with RTA v1.18.5 PGCGROWTHCONDITIONS
Cells were inoculated from frozen cultures into 5 mL of LB, and grown.  5 µL of this overnight culture was diluted into 5 mL of LB with the appropriate concentration of arabinose, and grown for 20h. PGCGROWTHCONDITIONS
E. coli culture PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Reads were mapped using BWA 0.7.5a PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was purified from 200 µL of overnight culture by pelleting and resuspeding in 500 µL of Trizol at 65°C, followed by purification on a column (Direct-Zol, Zymo Research). Samples received two 30-minute DNase treatments using TURBO DNA-free (Ambion) following the manufacturers instructions. RNA samples were then purified on a column (RNA Clean & Concentrator, Zymo Research). Three samples were prepped from each culture and pooled to generate sufficient RNA. PGCGROWTHCONDITIONS
rpos level: 100% PGCGROWTHCONDITIONS
strain: BW27786 (K-12 derivative) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: A tab deliminited file with counts for each gene. PGCGROWTHCONDITIONS
the first ten base pairs of each read were trimmed using FASTX­Toolkit 0.0.13. PGCGROWTHCONDITIONS
The number read pairs mapped to each gene was counted with HTSeq 0.6.1 PGCGROWTHCONDITIONS
0% rep1 PGCGROWTHCONDITIONS
Base calls performed with RTA v1.18.5 PGCGROWTHCONDITIONS
Cells were inoculated from frozen cultures into 5 mL of LB, and grown.  5 µL of this overnight culture was diluted into 5 mL of LB with the appropriate concentration of arabinose, and grown for 20h. PGCGROWTHCONDITIONS
E. coli culture PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Reads were mapped using BWA 0.7.5a PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was purified from 200 µL of overnight culture by pelleting and resuspeding in 500 µL of Trizol at 65°C, followed by purification on a column (Direct-Zol, Zymo Research). Samples received two 30-minute DNase treatments using TURBO DNA-free (Ambion) following the manufacturers instructions. RNA samples were then purified on a column (RNA Clean & Concentrator, Zymo Research). Three samples were prepped from each culture and pooled to generate sufficient RNA. PGCGROWTHCONDITIONS
rpos level: 0% PGCGROWTHCONDITIONS
strain: DMS2545 (K-12 derivative) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: A tab deliminited file with counts for each gene. PGCGROWTHCONDITIONS
the first ten base pairs of each read were trimmed using FASTX­Toolkit 0.0.13. PGCGROWTHCONDITIONS
The number read pairs mapped to each gene was counted with HTSeq 0.6.1 PGCGROWTHCONDITIONS
26% rep1 PGCGROWTHCONDITIONS
Base calls performed with RTA v1.18.5 PGCGROWTHCONDITIONS
Cells were inoculated from frozen cultures into 5 mL of LB, and grown.  5 µL of this overnight culture was diluted into 5 mL of LB with the appropriate concentration of arabinose, and grown for 20h. PGCGROWTHCONDITIONS
E. coli culture PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Reads were mapped using BWA 0.7.5a PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was purified from 200 µL of overnight culture by pelleting and resuspeding in 500 µL of Trizol at 65°C, followed by purification on a column (Direct-Zol, Zymo Research). Samples received two 30-minute DNase treatments using TURBO DNA-free (Ambion) following the manufacturers instructions. RNA samples were then purified on a column (RNA Clean & Concentrator, Zymo Research). Three samples were prepped from each culture and pooled to generate sufficient RNA. PGCGROWTHCONDITIONS
rpos level: 26% PGCGROWTHCONDITIONS
strain: DMS2564 (K-12 derivative) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: A tab deliminited file with counts for each gene. PGCGROWTHCONDITIONS
the first ten base pairs of each read were trimmed using FASTX­Toolkit 0.0.13. PGCGROWTHCONDITIONS
The number read pairs mapped to each gene was counted with HTSeq 0.6.1 PGCGROWTHCONDITIONS
100% rep2 PGCGROWTHCONDITIONS
Base calls performed with RTA v1.18.5 PGCGROWTHCONDITIONS
Cells were inoculated from frozen cultures into 5 mL of LB, and grown.  5 µL of this overnight culture was diluted into 5 mL of LB with the appropriate concentration of arabinose, and grown for 20h. PGCGROWTHCONDITIONS
E. coli culture PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Reads were mapped using BWA 0.7.5a PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was purified from 200 µL of overnight culture by pelleting and resuspeding in 500 µL of Trizol at 65°C, followed by purification on a column (Direct-Zol, Zymo Research). Samples received two 30-minute DNase treatments using TURBO DNA-free (Ambion) following the manufacturers instructions. RNA samples were then purified on a column (RNA Clean & Concentrator, Zymo Research). Three samples were prepped from each culture and pooled to generate sufficient RNA. PGCGROWTHCONDITIONS
rpos level: 100% PGCGROWTHCONDITIONS
strain: BW27786 (K-12 derivative) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: A tab deliminited file with counts for each gene. PGCGROWTHCONDITIONS
the first ten base pairs of each read were trimmed using FASTX­Toolkit 0.0.13. PGCGROWTHCONDITIONS
The number read pairs mapped to each gene was counted with HTSeq 0.6.1 PGCGROWTHCONDITIONS
0% rep2 PGCGROWTHCONDITIONS
Base calls performed with RTA v1.18.5 PGCGROWTHCONDITIONS
Cells were inoculated from frozen cultures into 5 mL of LB, and grown.  5 µL of this overnight culture was diluted into 5 mL of LB with the appropriate concentration of arabinose, and grown for 20h. PGCGROWTHCONDITIONS
E. coli culture PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Reads were mapped using BWA 0.7.5a PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was purified from 200 µL of overnight culture by pelleting and resuspeding in 500 µL of Trizol at 65°C, followed by purification on a column (Direct-Zol, Zymo Research). Samples received two 30-minute DNase treatments using TURBO DNA-free (Ambion) following the manufacturers instructions. RNA samples were then purified on a column (RNA Clean & Concentrator, Zymo Research). Three samples were prepped from each culture and pooled to generate sufficient RNA. PGCGROWTHCONDITIONS
rpos level: 0% PGCGROWTHCONDITIONS
strain: DMS2545 (K-12 derivative) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: A tab deliminited file with counts for each gene. PGCGROWTHCONDITIONS
the first ten base pairs of each read were trimmed using FASTX­Toolkit 0.0.13. PGCGROWTHCONDITIONS
The number read pairs mapped to each gene was counted with HTSeq 0.6.1 PGCGROWTHCONDITIONS
26% rep2 PGCGROWTHCONDITIONS
Base calls performed with RTA v1.18.5 PGCGROWTHCONDITIONS
Cells were inoculated from frozen cultures into 5 mL of LB, and grown.  5 µL of this overnight culture was diluted into 5 mL of LB with the appropriate concentration of arabinose, and grown for 20h. PGCGROWTHCONDITIONS
E. coli culture PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Reads were mapped using BWA 0.7.5a PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was purified from 200 µL of overnight culture by pelleting and resuspeding in 500 µL of Trizol at 65°C, followed by purification on a column (Direct-Zol, Zymo Research). Samples received two 30-minute DNase treatments using TURBO DNA-free (Ambion) following the manufacturers instructions. RNA samples were then purified on a column (RNA Clean & Concentrator, Zymo Research). Three samples were prepped from each culture and pooled to generate sufficient RNA. PGCGROWTHCONDITIONS
rpos level: 26% PGCGROWTHCONDITIONS
strain: DMS2564 (K-12 derivative) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: A tab deliminited file with counts for each gene. PGCGROWTHCONDITIONS
the first ten base pairs of each read were trimmed using FASTX­Toolkit 0.0.13. PGCGROWTHCONDITIONS
The number read pairs mapped to each gene was counted with HTSeq 0.6.1 PGCGROWTHCONDITIONS
A Linker-1 adapter (IDT) was ligated onto the 3' end of size selected RNA fragments, either ribosome footprints or fragmented total RNA. A cDNA library was created using Superscript III (ThermoFisher). After gel purification of the cDNA library all ssDNA fragments were circularized using CircLigase (Epicentre). For ribosome profiling samples rRNA containing circles were depleted using oligo-biotin  and streptavidin coupled Dynabeads (ThermoFisher) subtraction. A PCR amplification off the circles using HF Phusion (NEB) completed the libraries by adding Illumina Tru-Seq adapters and a unique index for each sample. PGCGROWTHCONDITIONS
All strains were grown shaking at 37°C  in 200mL cultures of MOPS complete-glucose liquid media (unless otherwise annotated) in 1L flasks and cells were harvested at OD(420nm) between 0.4 - 0.6 PGCGROWTHCONDITIONS
Cells from each strain were rapidly harvested by filtration and lysate was produced by pulverization of liquid nitrogen cooled samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
Reads were aligned to E.coli rRNA and tRNA using Bowtie v.0.12.0 allowing for one mismatch and reads aligning to more than one position in the genome were randomly assigned to one of those positions PGCGROWTHCONDITIONS
Remaining linker-1 reads (CTGTAGGCACCATCAAT) were removed from fastq files using fastx_clipper PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K12 MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Bedgraph wiggle files were created for each sample and replicate for all reads aligned to the genome after computational rRNA and tRNA subtraction PGCGROWTHCONDITIONS
The aligned reads were converted to BAM files and sorted and indexed using SAMtools PGCGROWTHCONDITIONS
The remaining reads were aligned to genome using Bowtie v.0.12.0 allowing for one mismatch and reads aligning in more than one position in the genome were discarded PGCGROWTHCONDITIONS
whole cell lysate PGCGROWTHCONDITIONS
Whole cell lysates were clarified by brief centrifugation. Ribosome footprints were created using Mnase digestion (45 enzyme units per absorbance unit of lysate at 260nm). Using sucrose gradients the monosome fraction of lysate was isolated and footprints were size selected and converted to a cDNA library. Total RNA was extracted from purified lysate for a simultaneous RNA-seq library production for total RNA samples. Small RNA and ribosomal RNA subtraction was performed in total RNA samples using MEGAClear (ThermoFisher) and MicrobExpress (ThermoFisher) kits. Subtracted total RNA was then subjected to alkaline fragmentation prior to library preparation. PGCGROWTHCONDITIONS
Wiggle files were created by center mapping the reads between 20-40bps. Using a 10bp trim on either side of the read then mapping the read across the remaining location using Plastid. PGCGROWTHCONDITIONS
WT_exp1_mRNA PGCGROWTHCONDITIONS
A Linker-1 adapter (IDT) was ligated onto the 3' end of size selected RNA fragments, either ribosome footprints or fragmented total RNA. A cDNA library was created using Superscript III (ThermoFisher). After gel purification of the cDNA library all ssDNA fragments were circularized using CircLigase (Epicentre). For ribosome profiling samples rRNA containing circles were depleted using oligo-biotin  and streptavidin coupled Dynabeads (ThermoFisher) subtraction. A PCR amplification off the circles using HF Phusion (NEB) completed the libraries by adding Illumina Tru-Seq adapters and a unique index for each sample. PGCGROWTHCONDITIONS
All strains were grown shaking at 37°C  in 200mL cultures of MOPS complete-glucose liquid media (unless otherwise annotated) in 1L flasks and cells were harvested at OD(420nm) between 0.4 - 0.6 PGCGROWTHCONDITIONS
Cells from each strain were rapidly harvested by filtration and lysate was produced by pulverization of liquid nitrogen cooled samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
Reads were aligned to E.coli rRNA and tRNA using Bowtie v.0.12.0 allowing for one mismatch and reads aligning to more than one position in the genome were randomly assigned to one of those positions PGCGROWTHCONDITIONS
Remaining linker-1 reads (CTGTAGGCACCATCAAT) were removed from fastq files using fastx_clipper PGCGROWTHCONDITIONS
∆RF3_exp1_mRNA PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K12 MG1655 deltaprfC PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Bedgraph wiggle files were created for each sample and replicate for all reads aligned to the genome after computational rRNA and tRNA subtraction PGCGROWTHCONDITIONS
The aligned reads were converted to BAM files and sorted and indexed using SAMtools PGCGROWTHCONDITIONS
The remaining reads were aligned to genome using Bowtie v.0.12.0 allowing for one mismatch and reads aligning in more than one position in the genome were discarded PGCGROWTHCONDITIONS
whole cell lysate PGCGROWTHCONDITIONS
Whole cell lysates were clarified by brief centrifugation. Ribosome footprints were created using Mnase digestion (45 enzyme units per absorbance unit of lysate at 260nm). Using sucrose gradients the monosome fraction of lysate was isolated and footprints were size selected and converted to a cDNA library. Total RNA was extracted from purified lysate for a simultaneous RNA-seq library production for total RNA samples. Small RNA and ribosomal RNA subtraction was performed in total RNA samples using MEGAClear (ThermoFisher) and MicrobExpress (ThermoFisher) kits. Subtracted total RNA was then subjected to alkaline fragmentation prior to library preparation. PGCGROWTHCONDITIONS
Wiggle files were created by center mapping the reads between 20-40bps. Using a 10bp trim on either side of the read then mapping the read across the remaining location using Plastid. PGCGROWTHCONDITIONS
A Linker-1 adapter (IDT) was ligated onto the 3' end of size selected RNA fragments, either ribosome footprints or fragmented total RNA. A cDNA library was created using Superscript III (ThermoFisher). After gel purification of the cDNA library all ssDNA fragments were circularized using CircLigase (Epicentre). For ribosome profiling samples rRNA containing circles were depleted using oligo-biotin  and streptavidin coupled Dynabeads (ThermoFisher) subtraction. A PCR amplification off the circles using HF Phusion (NEB) completed the libraries by adding Illumina Tru-Seq adapters and a unique index for each sample. PGCGROWTHCONDITIONS
All strains were grown shaking at 37°C  in 200mL cultures of MOPS complete-glucose liquid media (unless otherwise annotated) in 1L flasks and cells were harvested at OD(420nm) between 0.4 - 0.6 PGCGROWTHCONDITIONS
Cells from each strain were rapidly harvested by filtration and lysate was produced by pulverization of liquid nitrogen cooled samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913 PGCGROWTHCONDITIONS
Reads were aligned to E.coli rRNA and tRNA using Bowtie v.0.12.0 allowing for one mismatch and reads aligning to more than one position in the genome were randomly assigned to one of those positions PGCGROWTHCONDITIONS
Remaining linker-1 reads (CTGTAGGCACCATCAAT) were removed from fastq files using fastx_clipper PGCGROWTHCONDITIONS
RF2*_exp1_mRNA PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K12 MG1655 prfB-Bstrain allele PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Bedgraph wiggle files were created for each sample and replicate for all reads aligned to the genome after computational rRNA and tRNA subtraction PGCGROWTHCONDITIONS
The aligned reads were converted to BAM files and sorted and indexed using SAMtools PGCGROWTHCONDITIONS
The remaining reads were aligned to genome using Bowtie v.0.12.0 allowing for one mismatch and reads aligning in more than one position in the genome were discarded PGCGROWTHCONDITIONS
whole cell lysate PGCGROWTHCONDITIONS
Whole cell lysates were clarified by brief centrifugation. Ribosome footprints were created using Mnase digestion (45 enzyme units per absorbance unit of lysate at 260nm). Using sucrose gradients the monosome fraction of lysate was isolated and footprints were size selected and converted to a cDNA library. Total RNA was extracted from purified lysate for a simultaneous RNA-seq library production for total RNA samples. Small RNA and ribosomal RNA subtraction was performed in total RNA samples using MEGAClear (ThermoFisher) and MicrobExpress (ThermoFisher) kits. Subtracted total RNA was then subjected to alkaline fragmentation prior to library preparation. PGCGROWTHCONDITIONS
Wiggle files were created by center mapping the reads between 20-40bps. Using a 10bp trim on either side of the read then mapping the read across the remaining location using Plastid. PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
Tube state 1 (IPTG-/aTc-/Ara-) PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
Tube state 2 (IPTG+/aTc-/Ara-) PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
Tube state 3 (IPTG-/aTc+/Ara-) PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
Tube state 4 (IPTG+/aTc+/Ara-) PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
Tube state 5 (IPTG-/aTc-/Ara+) PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
Tube state 6 (IPTG+/aTc-/Ara+) PGCGROWTHCONDITIONS
Culture grown in 250 ml Erlenmeyer flask PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Flask state 1 (IPTG-/aTc-/Ara-) PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
Culture grown in 250 ml Erlenmeyer flask PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Flask state 2 (IPTG+/aTc-/Ara-) PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
Culture grown in 250 ml Erlenmeyer flask PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Flask state 3 (IPTG-/aTc+/Ara-) PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
Culture grown in 250 ml Erlenmeyer flask PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Flask state 4 (IPTG+/aTc+/Ara-) PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
Culture grown in 250 ml Erlenmeyer flask PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Flask state 5 (IPTG-/aTc-/Ara+) PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
Culture grown in 250 ml Erlenmeyer flask PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Flask state 6 (IPTG+/aTc-/Ara+) PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
Culture grown in 250 ml Erlenmeyer flask PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Flask state 7 (IPTG-/aTc+/Ara+) PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
Culture grown in 250 ml Erlenmeyer flask PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Flask state 8 (IPTG+/aTc+/Ara+) PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
0min minus ciprofloxacin PGCGROWTHCONDITIONS
All data was processed using Rockhopper Ver.2.03. Rockhopper is an utomatic\ bacterial RNA-seq analysis tool; for additional information see: McClure, R., et al. (2013). \Computational analysis of bacterial RNA-Seq data.\ Nucleic Acids Res 41(14): e140. The default general parameters were used with the erbose output\ tab ticked and the \orientation of mate-pair reads\ changed to 
f\. PGCGROWTHCONDITIONS
Clinical isolate, minus ciprofloxacin, 0min PGCGROWTHCONDITIONS
E. coli ST131 UR40 was treated with ciprofloxacin (2µg/mL) and samples were taken at time points 0 min, 30 min and 90min. PGCGROWTHCONDITIONS
Escherichia coli O25b:H4-ST131 PGCGROWTHCONDITIONS
Extraction followed by DNase treatment with TURBO DNA-free kit from Ambion. rRNA depleted using an Illumina Ribo-zero rRNA removal kit. Followed by RNA-seq library prep using an Illumina TruSeq Stranded mRNA Library Prep Kit. PGCGROWTHCONDITIONS
Genome_build: NC_017644.1 (Escherichia coli NA114) PGCGROWTHCONDITIONS
isolate: UR40 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: *txt, *xml: These files contain the raw counts, normalized counts, RPKM values, expression values, P-values and Q-values. Each file contains the values for both samples at the indicated timepoint. PGCGROWTHCONDITIONS
The cultures were balanced and grown in CAMHB media at 37 degrees Celsius. PGCGROWTHCONDITIONS
time point: 0min PGCGROWTHCONDITIONS
Total RNA was extracted using a Thermo Scientific GeneJET RNA isolation kit. PGCGROWTHCONDITIONS
treatment: none PGCGROWTHCONDITIONS
0min plus ciprofloxacin PGCGROWTHCONDITIONS
All data was processed using Rockhopper Ver.2.03. Rockhopper is an utomatic\ bacterial RNA-seq analysis tool; for additional information see: McClure, R., et al. (2013). \Computational analysis of bacterial RNA-Seq data.\ Nucleic Acids Res 41(14): e140. The default general parameters were used with the erbose output\ tab ticked and the \orientation of mate-pair reads\ changed to 
f\. PGCGROWTHCONDITIONS
Clinical isolate, plus ciprofloxacin, 0min PGCGROWTHCONDITIONS
E. coli ST131 UR40 was treated with ciprofloxacin (2µg/mL) and samples were taken at time points 0 min, 30 min and 90min. PGCGROWTHCONDITIONS
Escherichia coli O25b:H4-ST131 PGCGROWTHCONDITIONS
Extraction followed by DNase treatment with TURBO DNA-free kit from Ambion. rRNA depleted using an Illumina Ribo-zero rRNA removal kit. Followed by RNA-seq library prep using an Illumina TruSeq Stranded mRNA Library Prep Kit. PGCGROWTHCONDITIONS
Genome_build: NC_017644.1 (Escherichia coli NA114) PGCGROWTHCONDITIONS
isolate: UR40 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: *txt, *xml: These files contain the raw counts, normalized counts, RPKM values, expression values, P-values and Q-values. Each file contains the values for both samples at the indicated timepoint. PGCGROWTHCONDITIONS
The cultures were balanced and grown in CAMHB media at 37 degrees Celsius. PGCGROWTHCONDITIONS
time point: 0min PGCGROWTHCONDITIONS
Total RNA was extracted using a Thermo Scientific GeneJET RNA isolation kit. PGCGROWTHCONDITIONS
treatment: ciprofloxacin PGCGROWTHCONDITIONS
30min minus ciprofloxacin PGCGROWTHCONDITIONS
All data was processed using Rockhopper Ver.2.03. Rockhopper is an utomatic\ bacterial RNA-seq analysis tool; for additional information see: McClure, R., et al. (2013). \Computational analysis of bacterial RNA-Seq data.\ Nucleic Acids Res 41(14): e140. The default general parameters were used with the erbose output\ tab ticked and the \orientation of mate-pair reads\ changed to 
f\. PGCGROWTHCONDITIONS
Clinical isolate, minus ciprofloxacin, 30min PGCGROWTHCONDITIONS
E. coli ST131 UR40 was treated with ciprofloxacin (2µg/mL) and samples were taken at time points 0 min, 30 min and 90min. PGCGROWTHCONDITIONS
Escherichia coli O25b:H4-ST131 PGCGROWTHCONDITIONS
Extraction followed by DNase treatment with TURBO DNA-free kit from Ambion. rRNA depleted using an Illumina Ribo-zero rRNA removal kit. Followed by RNA-seq library prep using an Illumina TruSeq Stranded mRNA Library Prep Kit. PGCGROWTHCONDITIONS
Genome_build: NC_017644.1 (Escherichia coli NA114) PGCGROWTHCONDITIONS
isolate: UR40 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: *txt, *xml: These files contain the raw counts, normalized counts, RPKM values, expression values, P-values and Q-values. Each file contains the values for both samples at the indicated timepoint. PGCGROWTHCONDITIONS
The cultures were balanced and grown in CAMHB media at 37 degrees Celsius. PGCGROWTHCONDITIONS
time point: 30min PGCGROWTHCONDITIONS
Total RNA was extracted using a Thermo Scientific GeneJET RNA isolation kit. PGCGROWTHCONDITIONS
treatment: none PGCGROWTHCONDITIONS
30min plus ciprofloxacin PGCGROWTHCONDITIONS
All data was processed using Rockhopper Ver.2.03. Rockhopper is an utomatic\ bacterial RNA-seq analysis tool; for additional information see: McClure, R., et al. (2013). \Computational analysis of bacterial RNA-Seq data.\ Nucleic Acids Res 41(14): e140. The default general parameters were used with the erbose output\ tab ticked and the \orientation of mate-pair reads\ changed to 
f\. PGCGROWTHCONDITIONS
Clinical isolate, plus ciprofloxacin, 30min PGCGROWTHCONDITIONS
E. coli ST131 UR40 was treated with ciprofloxacin (2µg/mL) and samples were taken at time points 0 min, 30 min and 90min. PGCGROWTHCONDITIONS
Escherichia coli O25b:H4-ST131 PGCGROWTHCONDITIONS
Extraction followed by DNase treatment with TURBO DNA-free kit from Ambion. rRNA depleted using an Illumina Ribo-zero rRNA removal kit. Followed by RNA-seq library prep using an Illumina TruSeq Stranded mRNA Library Prep Kit. PGCGROWTHCONDITIONS
Genome_build: NC_017644.1 (Escherichia coli NA114) PGCGROWTHCONDITIONS
isolate: UR40 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: *txt, *xml: These files contain the raw counts, normalized counts, RPKM values, expression values, P-values and Q-values. Each file contains the values for both samples at the indicated timepoint. PGCGROWTHCONDITIONS
The cultures were balanced and grown in CAMHB media at 37 degrees Celsius. PGCGROWTHCONDITIONS
time point: 30min PGCGROWTHCONDITIONS
Total RNA was extracted using a Thermo Scientific GeneJET RNA isolation kit. PGCGROWTHCONDITIONS
treatment: ciprofloxacin PGCGROWTHCONDITIONS
90min minus ciprofloxacin PGCGROWTHCONDITIONS
All data was processed using Rockhopper Ver.2.03. Rockhopper is an utomatic\ bacterial RNA-seq analysis tool; for additional information see: McClure, R., et al. (2013). \Computational analysis of bacterial RNA-Seq data.\ Nucleic Acids Res 41(14): e140. The default general parameters were used with the erbose output\ tab ticked and the \orientation of mate-pair reads\ changed to 
f\. PGCGROWTHCONDITIONS
Clinical isolate, minus ciprofloxacin, 90min PGCGROWTHCONDITIONS
E. coli ST131 UR40 was treated with ciprofloxacin (2µg/mL) and samples were taken at time points 0 min, 30 min and 90min. PGCGROWTHCONDITIONS
Escherichia coli O25b:H4-ST131 PGCGROWTHCONDITIONS
Extraction followed by DNase treatment with TURBO DNA-free kit from Ambion. rRNA depleted using an Illumina Ribo-zero rRNA removal kit. Followed by RNA-seq library prep using an Illumina TruSeq Stranded mRNA Library Prep Kit. PGCGROWTHCONDITIONS
Genome_build: NC_017644.1 (Escherichia coli NA114) PGCGROWTHCONDITIONS
isolate: UR40 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: *txt, *xml: These files contain the raw counts, normalized counts, RPKM values, expression values, P-values and Q-values. Each file contains the values for both samples at the indicated timepoint. PGCGROWTHCONDITIONS
The cultures were balanced and grown in CAMHB media at 37 degrees Celsius. PGCGROWTHCONDITIONS
time point: 90min PGCGROWTHCONDITIONS
Total RNA was extracted using a Thermo Scientific GeneJET RNA isolation kit. PGCGROWTHCONDITIONS
treatment: none PGCGROWTHCONDITIONS
90min plus ciprofloxacin PGCGROWTHCONDITIONS
All data was processed using Rockhopper Ver.2.03. Rockhopper is an utomatic\ bacterial RNA-seq analysis tool; for additional information see: McClure, R., et al. (2013). \Computational analysis of bacterial RNA-Seq data.\ Nucleic Acids Res 41(14): e140. The default general parameters were used with the erbose output\ tab ticked and the \orientation of mate-pair reads\ changed to 
f\. PGCGROWTHCONDITIONS
Clinical isolate, plus ciprofloxacin, 90min PGCGROWTHCONDITIONS
E. coli ST131 UR40 was treated with ciprofloxacin (2µg/mL) and samples were taken at time points 0 min, 30 min and 90min. PGCGROWTHCONDITIONS
Escherichia coli O25b:H4-ST131 PGCGROWTHCONDITIONS
Extraction followed by DNase treatment with TURBO DNA-free kit from Ambion. rRNA depleted using an Illumina Ribo-zero rRNA removal kit. Followed by RNA-seq library prep using an Illumina TruSeq Stranded mRNA Library Prep Kit. PGCGROWTHCONDITIONS
Genome_build: NC_017644.1 (Escherichia coli NA114) PGCGROWTHCONDITIONS
isolate: UR40 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: *txt, *xml: These files contain the raw counts, normalized counts, RPKM values, expression values, P-values and Q-values. Each file contains the values for both samples at the indicated timepoint. PGCGROWTHCONDITIONS
The cultures were balanced and grown in CAMHB media at 37 degrees Celsius. PGCGROWTHCONDITIONS
time point: 90min PGCGROWTHCONDITIONS
Total RNA was extracted using a Thermo Scientific GeneJET RNA isolation kit. PGCGROWTHCONDITIONS
treatment: ciprofloxacin PGCGROWTHCONDITIONS
Basecalls performed using Illumina CASAVA. PGCGROWTHCONDITIONS
Cells were induced with arabinose or heat shocked, then harvested and flash frozen. PGCGROWTHCONDITIONS
Cells were lysed in liquid nitrogen, then samples were taken for total RNA. PGCGROWTHCONDITIONS
E. coli cultures PGCGROWTHCONDITIONS
ecoli_k12_42C_20min_m_1 PGCGROWTHCONDITIONS
E. coli were grown in defined rich media at 30C. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
growth temperature: 30C PGCGROWTHCONDITIONS
heat shock time: 20min PGCGROWTHCONDITIONS
induction: None PGCGROWTHCONDITIONS
plasmid: None PGCGROWTHCONDITIONS
Reads were aligned to the MG1655 genome with Bowtie. PGCGROWTHCONDITIONS
Reads were trimmed and adaptors removed using the fastx_toolkit. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was dephosphorylated, ligated to an adaptor, reverse transcribed, circularized then amplified with Illumina adaptors and barcodes. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: ecoli_heatshock_normalizedcounts.txt: Tab-delimited text file has EdgeR-normalized counts per kilobase million for each E. coli gene (EcoCyc gene names). PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: ecoli_heatshock_rawcounts.txt: Tab-delimited text file has raw read counts per kilobase million for each E. coli gene (EcoCyc gene names). PGCGROWTHCONDITIONS
The number of reads at each position in the genome was counted using in-house Python scripts. PGCGROWTHCONDITIONS
The number of reads mapping to each gene was counted and normalized using EdgeR. PGCGROWTHCONDITIONS
Total RNA was extracted with phenol chloroform and alkaline fragmented, then fragments (20-40 nt) were gel-purified. PGCGROWTHCONDITIONS
treatment temperature: 42C PGCGROWTHCONDITIONS
Basecalls performed using Illumina CASAVA. PGCGROWTHCONDITIONS
Cells were induced with arabinose or heat shocked, then harvested and flash frozen. PGCGROWTHCONDITIONS
Cells were lysed in liquid nitrogen, then samples were taken for total RNA. PGCGROWTHCONDITIONS
E. coli cultures PGCGROWTHCONDITIONS
ecoli_k12_42C_20min_m_3 PGCGROWTHCONDITIONS
E. coli were grown in defined rich media at 30C. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
growth temperature: 30C PGCGROWTHCONDITIONS
heat shock time: 20min PGCGROWTHCONDITIONS
induction: None PGCGROWTHCONDITIONS
plasmid: None PGCGROWTHCONDITIONS
Reads were aligned to the MG1655 genome with Bowtie. PGCGROWTHCONDITIONS
Reads were trimmed and adaptors removed using the fastx_toolkit. PGCGROWTHCONDITIONS
replicate: 3 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was dephosphorylated, ligated to an adaptor, reverse transcribed, circularized then amplified with Illumina adaptors and barcodes. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: ecoli_heatshock_normalizedcounts.txt: Tab-delimited text file has EdgeR-normalized counts per kilobase million for each E. coli gene (EcoCyc gene names). PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: ecoli_heatshock_rawcounts.txt: Tab-delimited text file has raw read counts per kilobase million for each E. coli gene (EcoCyc gene names). PGCGROWTHCONDITIONS
The number of reads at each position in the genome was counted using in-house Python scripts. PGCGROWTHCONDITIONS
The number of reads mapping to each gene was counted and normalized using EdgeR. PGCGROWTHCONDITIONS
Total RNA was extracted with phenol chloroform and alkaline fragmented, then fragments (20-40 nt) were gel-purified. PGCGROWTHCONDITIONS
treatment temperature: 42C PGCGROWTHCONDITIONS
All data analysis was performed using Rockhopper (McClure et al., 2013) and Escherichia coli str. K-12 substr. MG1655 as the reference genome. PGCGROWTHCONDITIONS
Blue_1 PGCGROWTHCONDITIONS
Data were visualized in the Rockhopper IGV genome browser (McClure et al., 2013) and TreeView 3.0 (Saldana et al., 2004). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth protocol: Log-phase culture (LB broth, Miller formulation) inoculated with one blue colony and grown for 5 hr at 37 degrees celsius PGCGROWTHCONDITIONS
Log-phase cultures (LB broth, Miller formulation) inoculated with either blue or pale colonies were grown for 5 hr at 37 degrees celsius.  Cells were pelleted by centrifugation and flash frozen on dry ice. PGCGROWTHCONDITIONS
parent strain: BW27785 PGCGROWTHCONDITIONS
phenotype: Blue colony-color (prion-containing) PGCGROWTHCONDITIONS
Purified total RNA was depleted of rRNA using a Ribo-Zero (Bacteria) rRNA Removal Kit (Illumina).  cDNA libraries were constructed and sequenced on an Illumina NextSeq 500 sequencer at the Harvard Biopolymers Facility. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Specifically, data were treated as two experiments constituting either two (lue\ cell transcriptomes) or three (\pale\ cell transcriptomes) biological replicates. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file includes Rockhopper (McClure et al., 2013) normalized transcript abundance measurements (Expression), transcript abundance ratios (Expression Ratio), and qValues (qValue) for raw data that were treated as two experiments constituting either two (lue\ cell transcriptomes; Blue_1.fastq, Blue_2.fastq) or three (\pale\ cell transcriptomes; Pale_1.fastq, Pale_2.fastq, Pale_3.fastq) biological replicates.  Gene annotation, gene product description, and strand information is also included. PGCGROWTHCONDITIONS
Total RNA extracted from Rho prion-containing cells PGCGROWTHCONDITIONS
Total RNA was extracted from cell pellets with TRI Reagent (MRC).  RNA was precipitated, resuspended in DNase Reaction Buffer (Invitrogen) for 30 min at room temperature.  DNase-treated samples were subsequently purified with an Rneasy Plus Mini Kit (Qiagen). PGCGROWTHCONDITIONS
All data analysis was performed using Rockhopper (McClure et al., 2013) and Escherichia coli str. K-12 substr. MG1655 as the reference genome. PGCGROWTHCONDITIONS
Blue_2 PGCGROWTHCONDITIONS
Data were visualized in the Rockhopper IGV genome browser (McClure et al., 2013) and TreeView 3.0 (Saldana et al., 2004). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth protocol: Log-phase culture (LB broth, Miller formulation) inoculated with one blue colony and grown for 5 hr at 37 degrees celsius PGCGROWTHCONDITIONS
Log-phase cultures (LB broth, Miller formulation) inoculated with either blue or pale colonies were grown for 5 hr at 37 degrees celsius.  Cells were pelleted by centrifugation and flash frozen on dry ice. PGCGROWTHCONDITIONS
parent strain: BW27785 PGCGROWTHCONDITIONS
phenotype: Blue colony-color (prion-containing) PGCGROWTHCONDITIONS
Purified total RNA was depleted of rRNA using a Ribo-Zero (Bacteria) rRNA Removal Kit (Illumina).  cDNA libraries were constructed and sequenced on an Illumina NextSeq 500 sequencer at the Harvard Biopolymers Facility. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Specifically, data were treated as two experiments constituting either two (lue\ cell transcriptomes) or three (\pale\ cell transcriptomes) biological replicates. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file includes Rockhopper (McClure et al., 2013) normalized transcript abundance measurements (Expression), transcript abundance ratios (Expression Ratio), and qValues (qValue) for raw data that were treated as two experiments constituting either two (lue\ cell transcriptomes; Blue_1.fastq, Blue_2.fastq) or three (\pale\ cell transcriptomes; Pale_1.fastq, Pale_2.fastq, Pale_3.fastq) biological replicates.  Gene annotation, gene product description, and strand information is also included. PGCGROWTHCONDITIONS
Total RNA extracted from Rho prion-containing cells PGCGROWTHCONDITIONS
Total RNA was extracted from cell pellets with TRI Reagent (MRC).  RNA was precipitated, resuspended in DNase Reaction Buffer (Invitrogen) for 30 min at room temperature.  DNase-treated samples were subsequently purified with an Rneasy Plus Mini Kit (Qiagen). PGCGROWTHCONDITIONS
All data analysis was performed using Rockhopper (McClure et al., 2013) and Escherichia coli str. K-12 substr. MG1655 as the reference genome. PGCGROWTHCONDITIONS
Data were visualized in the Rockhopper IGV genome browser (McClure et al., 2013) and TreeView 3.0 (Saldana et al., 2004). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth protocol: Log-phase culture (LB broth, Miller formulation) inoculated with one pale colony and grown for 5 hr at 37 degrees celsius PGCGROWTHCONDITIONS
Log-phase cultures (LB broth, Miller formulation) inoculated with either blue or pale colonies were grown for 5 hr at 37 degrees celsius.  Cells were pelleted by centrifugation and flash frozen on dry ice. PGCGROWTHCONDITIONS
Pale_1 PGCGROWTHCONDITIONS
parent strain: BW27785 PGCGROWTHCONDITIONS
phenotype: Pale colony-color (prion-lacking) PGCGROWTHCONDITIONS
Purified total RNA was depleted of rRNA using a Ribo-Zero (Bacteria) rRNA Removal Kit (Illumina).  cDNA libraries were constructed and sequenced on an Illumina NextSeq 500 sequencer at the Harvard Biopolymers Facility. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Specifically, data were treated as two experiments constituting either two (lue\ cell transcriptomes) or three (\pale\ cell transcriptomes) biological replicates. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file includes Rockhopper (McClure et al., 2013) normalized transcript abundance measurements (Expression), transcript abundance ratios (Expression Ratio), and qValues (qValue) for raw data that were treated as two experiments constituting either two (lue\ cell transcriptomes; Blue_1.fastq, Blue_2.fastq) or three (\pale\ cell transcriptomes; Pale_1.fastq, Pale_2.fastq, Pale_3.fastq) biological replicates.  Gene annotation, gene product description, and strand information is also included. PGCGROWTHCONDITIONS
Total RNA extracted from Rho prion-lacking cells PGCGROWTHCONDITIONS
Total RNA was extracted from cell pellets with TRI Reagent (MRC).  RNA was precipitated, resuspended in DNase Reaction Buffer (Invitrogen) for 30 min at room temperature.  DNase-treated samples were subsequently purified with an Rneasy Plus Mini Kit (Qiagen). PGCGROWTHCONDITIONS
All data analysis was performed using Rockhopper (McClure et al., 2013) and Escherichia coli str. K-12 substr. MG1655 as the reference genome. PGCGROWTHCONDITIONS
Data were visualized in the Rockhopper IGV genome browser (McClure et al., 2013) and TreeView 3.0 (Saldana et al., 2004). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: ASM584v2 PGCGROWTHCONDITIONS
growth protocol: Log-phase culture (LB broth, Miller formulation) inoculated with one pale colony and grown for 5 hr at 37 degrees celsius PGCGROWTHCONDITIONS
Log-phase cultures (LB broth, Miller formulation) inoculated with either blue or pale colonies were grown for 5 hr at 37 degrees celsius.  Cells were pelleted by centrifugation and flash frozen on dry ice. PGCGROWTHCONDITIONS
Pale_3 PGCGROWTHCONDITIONS
parent strain: BW27785 PGCGROWTHCONDITIONS
phenotype: Pale colony-color (prion-lacking) PGCGROWTHCONDITIONS
Purified total RNA was depleted of rRNA using a Ribo-Zero (Bacteria) rRNA Removal Kit (Illumina).  cDNA libraries were constructed and sequenced on an Illumina NextSeq 500 sequencer at the Harvard Biopolymers Facility. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Specifically, data were treated as two experiments constituting either two (lue\ cell transcriptomes) or three (\pale\ cell transcriptomes) biological replicates. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Tab-delimited text file includes Rockhopper (McClure et al., 2013) normalized transcript abundance measurements (Expression), transcript abundance ratios (Expression Ratio), and qValues (qValue) for raw data that were treated as two experiments constituting either two (lue\ cell transcriptomes; Blue_1.fastq, Blue_2.fastq) or three (\pale\ cell transcriptomes; Pale_1.fastq, Pale_2.fastq, Pale_3.fastq) biological replicates.  Gene annotation, gene product description, and strand information is also included. PGCGROWTHCONDITIONS
Total RNA extracted from Rho prion-lacking cells PGCGROWTHCONDITIONS
Total RNA was extracted from cell pellets with TRI Reagent (MRC).  RNA was precipitated, resuspended in DNase Reaction Buffer (Invitrogen) for 30 min at room temperature.  DNase-treated samples were subsequently purified with an Rneasy Plus Mini Kit (Qiagen). PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 5min, rep1 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 5min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 10min, rep1 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 10min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 25min, rep1 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 25min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 45min, rep1 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 45min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 75min, rep1 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 75min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 120min, rep1 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 120min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 210min, rep1 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 210min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 330min, rep1 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 330min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 25h, rep1 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 25h PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 26h, rep1 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 26h PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 28h, rep1 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 28h PGCGROWTHCONDITIONS
chemostat STR culture PGCGROWTHCONDITIONS
chemostat STR culture STR  reference 1, rep1 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 0-16h PGCGROWTHCONDITIONS
chemostat STR culture PGCGROWTHCONDITIONS
chemostat STR culture STR  reference 2, rep1 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 0-15h PGCGROWTHCONDITIONS
chemostat STR culture PGCGROWTHCONDITIONS
chemostat STR culture STR  reference 3, rep1 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 0-2h PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 5min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P5 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 5min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 10min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P5 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 10min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 25min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P5 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 25min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P3 25min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P3 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 25min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P1 25min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P1 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 25min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 45min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P5 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 45min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 120min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P5 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 120min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P3 120min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P3 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 120min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P1 120min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P1 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 120min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 210min, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P5 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 210min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 25h, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P5 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 25h PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P3 28h, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P3 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 28h PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 28h, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P5 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 28h PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P1 28h, rep1 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 1 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P1 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 28h PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 5min, rep2 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 5min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 10min, rep2 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 10min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 25min, rep2 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 25min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 45min, rep2 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 45min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 75min, rep2 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 75min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 120min, rep2 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 120min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 210min, rep2 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 210min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 330min, rep2 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 330min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 25h, rep2 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 25h PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 26h, rep2 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 26h PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
chemostat STR-PFR culture STR 28h, rep2 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 28h PGCGROWTHCONDITIONS
chemostat STR culture PGCGROWTHCONDITIONS
chemostat STR culture STR reference 1 , rep2 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 0-16h PGCGROWTHCONDITIONS
chemostat STR culture PGCGROWTHCONDITIONS
chemostat STR culture STR reference 2 , rep2 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 0-15h PGCGROWTHCONDITIONS
chemostat STR culture PGCGROWTHCONDITIONS
chemostat STR culture STR reference 3 , rep2 PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: STR PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 0-2h PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 5min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P5 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 5min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 10min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P5 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 10min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 25min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P5 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 25min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P3 25min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P3 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 25min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P1 25min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P1 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 25min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 45min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P5 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 45min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 75min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P5 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 75min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 120min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P5 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 120min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P3 120min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P3 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 120min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P1 120min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P1 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 120min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 210min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P5 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 210min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 330min, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P5 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 330min PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 25h, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P5 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 25h PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 26h, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P5 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 26h PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P5 28h, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P5 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 28h PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P3 28h, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P3 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 28h PGCGROWTHCONDITIONS
chemostat STR-PFR culture PFR P1 28h, rep2 PGCGROWTHCONDITIONS
chemostat STR-PFR culture PGCGROWTHCONDITIONS
E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
replicate: 2 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
sample port: PFR P1 PGCGROWTHCONDITIONS
Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
strain: K12 W3110 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
time: 28h PGCGROWTHCONDITIONS
ATCACG-D1 PGCGROWTHCONDITIONS
DGE analysis used a false-discovery rate (FDR) of 0.10. PGCGROWTHCONDITIONS
Differential gene expression (DGE) was then performed on fragments per kilobase mapped (FPKM) values in Cufflinks’ Cuffdiff package (version 0.0.7). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For the whole-transcriptome analysis, sequencing was verified using FASTQC (version 0.11.2) to confirm base-call quality in each indexed file. PGCGROWTHCONDITIONS
Genome_build: FM180568 PGCGROWTHCONDITIONS
Genome_build: FM180569 PGCGROWTHCONDITIONS
Genome_build: FM180570 PGCGROWTHCONDITIONS
genotype/variation: {delta}perC::kanR, coisogenic to WT PGCGROWTHCONDITIONS
Incubation and RNA harvesting were carried out for all samples simultaneously and under RNase-free conditions to minimize biological variability in gene expression between each sample. Bacterial concentrations were equalized to the same density (by OD600). PGCGROWTHCONDITIONS
Indices corresponding to the same sample were merged, and then uploaded to a cloud-based variant of Galaxy named RNA23 Rocket PGCGROWTHCONDITIONS
LB (5 ml) was inoculated by a frozen stock of WT or perC-mutant strain and incubated at 37°C with 225 rpm shaking. Flasks containing low-glucose DMEM were inoculated 1:100 with the overnight culture and incubated at 37°C with 225 rpm shaking to mid-exponential phase (OD600 0.3-0.5). PGCGROWTHCONDITIONS
Mapped reads were quality checked with SAMstat (version 1.08), and transcripts were assembled in Cufflinks (version 2.0.2) PGCGROWTHCONDITIONS
Resulting mRNA was reverse-transcribed to cDNA libraries via SuperScript III First Strand reverse transcription kit (Invitrogen, Carlsbad, CA, 18080051) as per the manufacturer’s instructions. The cDNA libraries were multiplexed to distinguish replicates from one another, barcoded for sequencing, and then amplified with random hexamers for 15 PCR cycles. Transcripts were sequenced for 50 bases in single-end fashion within one lane of an Illumina Hiseq 2000 flow cell. This yielded roughly 30 million reads per sample. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were diluted 1:1 in RNA Protect (Qiagen, Carlsbad, CA) to inhibit RNase activity and then centrifuged (5000 x g, 10 min). Pellets were resuspended in TE/lysozyme (10 mg/ml lysozyme, 0.5% SDS, pH 8.0) with added proteinase K (1.5 mg/ml). RNA was isolated using Qiagen’s RNeasy kit according to manufacturer instructions with slight modification. Before centrifugation, β-mercaptoethanol was added to RNeasy kit buffer RLT (10% v/v). Additionally, during the wash step RNase-free DNase (Qiagen, Carlsbad, CA) was diluted in RNeasy kit buffer RDD (310 Kunitz units/mL), added to the purification column, and incubated for 15 minutes at room temperature (RT). After isolation, spectrophotometric NanoDrop (NanoDrop 1000 v3.8.1; Thermo Fisher) curves were obtained for each total RNA sample and verified for purity, as defined by absorbance ratios at 260/280 nm and 260/230 nm. Total RNA samples were sent to Oregon State University’s Center for Genome Research and Biocomputing. RNA integrity (RIN) measurements were taken using an Agilent Bioanalyzer, resulting in RIN scores of 10, out of a possible 10, for each sample. Ribosomal RNA was depleted using the RiboZero rRNA removal kit (Life Technologies, Eugene, OR). PGCGROWTHCONDITIONS
source: Bustamante et al., 2011 PGCGROWTHCONDITIONS
strain: JPEP22 PGCGROWTHCONDITIONS
Subsequent data visualizations were performed in R (version 3.1.2) using the cummeRbund package (version 3.0) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: bedgraph: Data presented in a 4 column BED format, of which the first column is the chromosome, the second column is the start position of the chromosome, the third column is the end position, and the fourth column is the fragments per kilobase mapped (FPKM) for that sample. Chromosome positions are specified as 0-relative. The first chromosome position is 0. The last position in a chromosome of length N would be N - 1. Only positions specified have data. Positions not specified do not have data and will not be graphed. All positions specified in the input data are in numerical order. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tabular: Tabular data that informs the excel spreadsheet. The data are averaged across the three samples per strain. Both averaged strain data are presented for each gene on the same line. Data contain gene ID, gene number, locus, fragments per kilobase mapped (FPKM) for WT and mutant strains, log2(fold-change) relative epxression of WT over mutant strains, test-statistic, p-value, q-value, and significance analyzed via the cummeRbund package in R whereby a q-value of <0.05 is considered significant. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xls: The data are averaged across the three samples per strain. Both averaged strain data are presented for each gene on the same line. Excel spreadsheet containing gene ID, gene number, locus, fragments per kilobase mapped (FPKM) for WT and mutant strains, log2(fold-change) relative epxression of WT over mutant strains, test-statistic, p-value, q-value, and significance analyzed via the cummeRbund package in R whereby a q-value of <0.05 is considered significant. PGCGROWTHCONDITIONS
Using Bowtie2 (version 2.0.2), sequenced reads were mapped to an EPEC O127:H6 reference genome (EMBL/GenBank accession codes FM180568, FM180569, and FM180570). PGCGROWTHCONDITIONS
Whole bacterial cell RNA transcriptome PGCGROWTHCONDITIONS
CGATGT-D2 PGCGROWTHCONDITIONS
DGE analysis used a false-discovery rate (FDR) of 0.10. PGCGROWTHCONDITIONS
Differential gene expression (DGE) was then performed on fragments per kilobase mapped (FPKM) values in Cufflinks’ Cuffdiff package (version 0.0.7). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For the whole-transcriptome analysis, sequencing was verified using FASTQC (version 0.11.2) to confirm base-call quality in each indexed file. PGCGROWTHCONDITIONS
Genome_build: FM180568 PGCGROWTHCONDITIONS
Genome_build: FM180569 PGCGROWTHCONDITIONS
Genome_build: FM180570 PGCGROWTHCONDITIONS
genotype/variation: {delta}perC::kanR, coisogenic to WT PGCGROWTHCONDITIONS
Incubation and RNA harvesting were carried out for all samples simultaneously and under RNase-free conditions to minimize biological variability in gene expression between each sample. Bacterial concentrations were equalized to the same density (by OD600). PGCGROWTHCONDITIONS
Indices corresponding to the same sample were merged, and then uploaded to a cloud-based variant of Galaxy named RNA23 Rocket PGCGROWTHCONDITIONS
LB (5 ml) was inoculated by a frozen stock of WT or perC-mutant strain and incubated at 37°C with 225 rpm shaking. Flasks containing low-glucose DMEM were inoculated 1:100 with the overnight culture and incubated at 37°C with 225 rpm shaking to mid-exponential phase (OD600 0.3-0.5). PGCGROWTHCONDITIONS
Mapped reads were quality checked with SAMstat (version 1.08), and transcripts were assembled in Cufflinks (version 2.0.2) PGCGROWTHCONDITIONS
Resulting mRNA was reverse-transcribed to cDNA libraries via SuperScript III First Strand reverse transcription kit (Invitrogen, Carlsbad, CA, 18080051) as per the manufacturer’s instructions. The cDNA libraries were multiplexed to distinguish replicates from one another, barcoded for sequencing, and then amplified with random hexamers for 15 PCR cycles. Transcripts were sequenced for 50 bases in single-end fashion within one lane of an Illumina Hiseq 2000 flow cell. This yielded roughly 30 million reads per sample. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were diluted 1:1 in RNA Protect (Qiagen, Carlsbad, CA) to inhibit RNase activity and then centrifuged (5000 x g, 10 min). Pellets were resuspended in TE/lysozyme (10 mg/ml lysozyme, 0.5% SDS, pH 8.0) with added proteinase K (1.5 mg/ml). RNA was isolated using Qiagen’s RNeasy kit according to manufacturer instructions with slight modification. Before centrifugation, β-mercaptoethanol was added to RNeasy kit buffer RLT (10% v/v). Additionally, during the wash step RNase-free DNase (Qiagen, Carlsbad, CA) was diluted in RNeasy kit buffer RDD (310 Kunitz units/mL), added to the purification column, and incubated for 15 minutes at room temperature (RT). After isolation, spectrophotometric NanoDrop (NanoDrop 1000 v3.8.1; Thermo Fisher) curves were obtained for each total RNA sample and verified for purity, as defined by absorbance ratios at 260/280 nm and 260/230 nm. Total RNA samples were sent to Oregon State University’s Center for Genome Research and Biocomputing. RNA integrity (RIN) measurements were taken using an Agilent Bioanalyzer, resulting in RIN scores of 10, out of a possible 10, for each sample. Ribosomal RNA was depleted using the RiboZero rRNA removal kit (Life Technologies, Eugene, OR). PGCGROWTHCONDITIONS
source: Bustamante et al., 2011 PGCGROWTHCONDITIONS
strain: JPEP22 PGCGROWTHCONDITIONS
Subsequent data visualizations were performed in R (version 3.1.2) using the cummeRbund package (version 3.0) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: bedgraph: Data presented in a 4 column BED format, of which the first column is the chromosome, the second column is the start position of the chromosome, the third column is the end position, and the fourth column is the fragments per kilobase mapped (FPKM) for that sample. Chromosome positions are specified as 0-relative. The first chromosome position is 0. The last position in a chromosome of length N would be N - 1. Only positions specified have data. Positions not specified do not have data and will not be graphed. All positions specified in the input data are in numerical order. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tabular: Tabular data that informs the excel spreadsheet. The data are averaged across the three samples per strain. Both averaged strain data are presented for each gene on the same line. Data contain gene ID, gene number, locus, fragments per kilobase mapped (FPKM) for WT and mutant strains, log2(fold-change) relative epxression of WT over mutant strains, test-statistic, p-value, q-value, and significance analyzed via the cummeRbund package in R whereby a q-value of <0.05 is considered significant. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xls: The data are averaged across the three samples per strain. Both averaged strain data are presented for each gene on the same line. Excel spreadsheet containing gene ID, gene number, locus, fragments per kilobase mapped (FPKM) for WT and mutant strains, log2(fold-change) relative epxression of WT over mutant strains, test-statistic, p-value, q-value, and significance analyzed via the cummeRbund package in R whereby a q-value of <0.05 is considered significant. PGCGROWTHCONDITIONS
Using Bowtie2 (version 2.0.2), sequenced reads were mapped to an EPEC O127:H6 reference genome (EMBL/GenBank accession codes FM180568, FM180569, and FM180570). PGCGROWTHCONDITIONS
Whole bacterial cell RNA transcriptome PGCGROWTHCONDITIONS
DGE analysis used a false-discovery rate (FDR) of 0.10. PGCGROWTHCONDITIONS
Differential gene expression (DGE) was then performed on fragments per kilobase mapped (FPKM) values in Cufflinks’ Cuffdiff package (version 0.0.7). PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
For the whole-transcriptome analysis, sequencing was verified using FASTQC (version 0.11.2) to confirm base-call quality in each indexed file. PGCGROWTHCONDITIONS
Genome_build: FM180568 PGCGROWTHCONDITIONS
Genome_build: FM180569 PGCGROWTHCONDITIONS
Genome_build: FM180570 PGCGROWTHCONDITIONS
genotype/variation: {delta}perC::kanR, coisogenic to WT PGCGROWTHCONDITIONS
Incubation and RNA harvesting were carried out for all samples simultaneously and under RNase-free conditions to minimize biological variability in gene expression between each sample. Bacterial concentrations were equalized to the same density (by OD600). PGCGROWTHCONDITIONS
Indices corresponding to the same sample were merged, and then uploaded to a cloud-based variant of Galaxy named RNA23 Rocket PGCGROWTHCONDITIONS
LB (5 ml) was inoculated by a frozen stock of WT or perC-mutant strain and incubated at 37°C with 225 rpm shaking. Flasks containing low-glucose DMEM were inoculated 1:100 with the overnight culture and incubated at 37°C with 225 rpm shaking to mid-exponential phase (OD600 0.3-0.5). PGCGROWTHCONDITIONS
Mapped reads were quality checked with SAMstat (version 1.08), and transcripts were assembled in Cufflinks (version 2.0.2) PGCGROWTHCONDITIONS
Resulting mRNA was reverse-transcribed to cDNA libraries via SuperScript III First Strand reverse transcription kit (Invitrogen, Carlsbad, CA, 18080051) as per the manufacturer’s instructions. The cDNA libraries were multiplexed to distinguish replicates from one another, barcoded for sequencing, and then amplified with random hexamers for 15 PCR cycles. Transcripts were sequenced for 50 bases in single-end fashion within one lane of an Illumina Hiseq 2000 flow cell. This yielded roughly 30 million reads per sample. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Samples were diluted 1:1 in RNA Protect (Qiagen, Carlsbad, CA) to inhibit RNase activity and then centrifuged (5000 x g, 10 min). Pellets were resuspended in TE/lysozyme (10 mg/ml lysozyme, 0.5% SDS, pH 8.0) with added proteinase K (1.5 mg/ml). RNA was isolated using Qiagen’s RNeasy kit according to manufacturer instructions with slight modification. Before centrifugation, β-mercaptoethanol was added to RNeasy kit buffer RLT (10% v/v). Additionally, during the wash step RNase-free DNase (Qiagen, Carlsbad, CA) was diluted in RNeasy kit buffer RDD (310 Kunitz units/mL), added to the purification column, and incubated for 15 minutes at room temperature (RT). After isolation, spectrophotometric NanoDrop (NanoDrop 1000 v3.8.1; Thermo Fisher) curves were obtained for each total RNA sample and verified for purity, as defined by absorbance ratios at 260/280 nm and 260/230 nm. Total RNA samples were sent to Oregon State University’s Center for Genome Research and Biocomputing. RNA integrity (RIN) measurements were taken using an Agilent Bioanalyzer, resulting in RIN scores of 10, out of a possible 10, for each sample. Ribosomal RNA was depleted using the RiboZero rRNA removal kit (Life Technologies, Eugene, OR). PGCGROWTHCONDITIONS
source: Bustamante et al., 2011 PGCGROWTHCONDITIONS
strain: JPEP22 PGCGROWTHCONDITIONS
Subsequent data visualizations were performed in R (version 3.1.2) using the cummeRbund package (version 3.0) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: bedgraph: Data presented in a 4 column BED format, of which the first column is the chromosome, the second column is the start position of the chromosome, the third column is the end position, and the fourth column is the fragments per kilobase mapped (FPKM) for that sample. Chromosome positions are specified as 0-relative. The first chromosome position is 0. The last position in a chromosome of length N would be N - 1. Only positions specified have data. Positions not specified do not have data and will not be graphed. All positions specified in the input data are in numerical order. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tabular: Tabular data that informs the excel spreadsheet. The data are averaged across the three samples per strain. Both averaged strain data are presented for each gene on the same line. Data contain gene ID, gene number, locus, fragments per kilobase mapped (FPKM) for WT and mutant strains, log2(fold-change) relative epxression of WT over mutant strains, test-statistic, p-value, q-value, and significance analyzed via the cummeRbund package in R whereby a q-value of <0.05 is considered significant. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: xls: The data are averaged across the three samples per strain. Both averaged strain data are presented for each gene on the same line. Excel spreadsheet containing gene ID, gene number, locus, fragments per kilobase mapped (FPKM) for WT and mutant strains, log2(fold-change) relative epxression of WT over mutant strains, test-statistic, p-value, q-value, and significance analyzed via the cummeRbund package in R whereby a q-value of <0.05 is considered significant. PGCGROWTHCONDITIONS
TTAGGC-D3 PGCGROWTHCONDITIONS
Using Bowtie2 (version 2.0.2), sequenced reads were mapped to an EPEC O127:H6 reference genome (EMBL/GenBank accession codes FM180568, FM180569, and FM180570). PGCGROWTHCONDITIONS
Whole bacterial cell RNA transcriptome PGCGROWTHCONDITIONS
BGI inhouse software “filter_fq” for basecalling and trimming PGCGROWTHCONDITIONS
Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol.  The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
E. coli MG1655 / pORF1 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build:  NC_000913 PGCGROWTHCONDITIONS
induction: induced 50 µM IPTG PGCGROWTHCONDITIONS
ORF1_1_IPTG PGCGROWTHCONDITIONS
Read-mapping was done with soap2.21. Mapping towards genes was done by the following parameters -m 0 -x 1000 -s 28 -l 32 -v 5 -r 2 -p 3 PGCGROWTHCONDITIONS
replicates: ORF1 replicate 1 / induced PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The columns in the processed files are the following in order:  GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process PGCGROWTHCONDITIONS
The cells for RNA extraction were immediately mixed with RNA Protect Bacterial reagent® (Qiagen) and processed by the RNAeasy Mini Kit (Qiagen) according to the manufacturers instructions. The cells for whole cell proteomics were chilled in ice-slush, pelleted at 14000 rpm, 4°C and the media was aspirated.  The cells were washed with 3×1.5 mL PBS with pelleting at as above in between. The final pellet was stored at -80°C until being shipped to the Proteomics Core Facility at University of Gothenburg for processing. The RNA was shipped to BGI for total RNA sequencing. PGCGROWTHCONDITIONS
The gene expression values were calculated as RPKM (reads per kilobase transcriptome per million mapped reads) by the inhouse BGI pipeline. PGCGROWTHCONDITIONS
The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
TruSeq PGCGROWTHCONDITIONS
BGI inhouse software “filter_fq” for basecalling and trimming PGCGROWTHCONDITIONS
Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol.  The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
E. coli MG1655 / pORF1 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build:  NC_000913 PGCGROWTHCONDITIONS
ORF1_1 PGCGROWTHCONDITIONS
Read-mapping was done with soap2.21. Mapping towards genes was done by the following parameters -m 0 -x 1000 -s 28 -l 32 -v 5 -r 2 -p 3 PGCGROWTHCONDITIONS
replicates: ORF1 replicate 1 / not induced PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The columns in the processed files are the following in order:  GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process PGCGROWTHCONDITIONS
The cells for RNA extraction were immediately mixed with RNA Protect Bacterial reagent® (Qiagen) and processed by the RNAeasy Mini Kit (Qiagen) according to the manufacturers instructions. The cells for whole cell proteomics were chilled in ice-slush, pelleted at 14000 rpm, 4°C and the media was aspirated.  The cells were washed with 3×1.5 mL PBS with pelleting at as above in between. The final pellet was stored at -80°C until being shipped to the Proteomics Core Facility at University of Gothenburg for processing. The RNA was shipped to BGI for total RNA sequencing. PGCGROWTHCONDITIONS
The gene expression values were calculated as RPKM (reads per kilobase transcriptome per million mapped reads) by the inhouse BGI pipeline. PGCGROWTHCONDITIONS
The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
TruSeq PGCGROWTHCONDITIONS
BGI inhouse software “filter_fq” for basecalling and trimming PGCGROWTHCONDITIONS
Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol.  The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
E. coli MG1655 / pORF1 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build:  NC_000913 PGCGROWTHCONDITIONS
induction: induced 50 µM IPTG PGCGROWTHCONDITIONS
ORF1_2_IPTG PGCGROWTHCONDITIONS
Read-mapping was done with soap2.21. Mapping towards genes was done by the following parameters -m 0 -x 1000 -s 28 -l 32 -v 5 -r 2 -p 3 PGCGROWTHCONDITIONS
replicates: ORF1 replicate 2 / induced PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The columns in the processed files are the following in order:  GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process PGCGROWTHCONDITIONS
The cells for RNA extraction were immediately mixed with RNA Protect Bacterial reagent® (Qiagen) and processed by the RNAeasy Mini Kit (Qiagen) according to the manufacturers instructions. The cells for whole cell proteomics were chilled in ice-slush, pelleted at 14000 rpm, 4°C and the media was aspirated.  The cells were washed with 3×1.5 mL PBS with pelleting at as above in between. The final pellet was stored at -80°C until being shipped to the Proteomics Core Facility at University of Gothenburg for processing. The RNA was shipped to BGI for total RNA sequencing. PGCGROWTHCONDITIONS
The gene expression values were calculated as RPKM (reads per kilobase transcriptome per million mapped reads) by the inhouse BGI pipeline. PGCGROWTHCONDITIONS
The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
TruSeq PGCGROWTHCONDITIONS
BGI inhouse software “filter_fq” for basecalling and trimming PGCGROWTHCONDITIONS
Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol.  The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
E. coli MG1655 / pORF1 PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build:  NC_000913 PGCGROWTHCONDITIONS
ORF1_2 PGCGROWTHCONDITIONS
Read-mapping was done with soap2.21. Mapping towards genes was done by the following parameters -m 0 -x 1000 -s 28 -l 32 -v 5 -r 2 -p 3 PGCGROWTHCONDITIONS
replicates: ORF1 replicate 2 / not induced PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The columns in the processed files are the following in order:  GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process PGCGROWTHCONDITIONS
The cells for RNA extraction were immediately mixed with RNA Protect Bacterial reagent® (Qiagen) and processed by the RNAeasy Mini Kit (Qiagen) according to the manufacturers instructions. The cells for whole cell proteomics were chilled in ice-slush, pelleted at 14000 rpm, 4°C and the media was aspirated.  The cells were washed with 3×1.5 mL PBS with pelleting at as above in between. The final pellet was stored at -80°C until being shipped to the Proteomics Core Facility at University of Gothenburg for processing. The RNA was shipped to BGI for total RNA sequencing. PGCGROWTHCONDITIONS
The gene expression values were calculated as RPKM (reads per kilobase transcriptome per million mapped reads) by the inhouse BGI pipeline. PGCGROWTHCONDITIONS
The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
TruSeq PGCGROWTHCONDITIONS
BGI inhouse software “filter_fq” for basecalling and trimming PGCGROWTHCONDITIONS
Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol.  The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
E. coli MG1655 / Svi3-3 comp. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build:  NC_000913 PGCGROWTHCONDITIONS
induction: induced 50 µM IPTG PGCGROWTHCONDITIONS
Read-mapping was done with soap2.21. Mapping towards genes was done by the following parameters -m 0 -x 1000 -s 28 -l 32 -v 5 -r 2 -p 3 PGCGROWTHCONDITIONS
replicates: Svi3-3 replicate 1 / induced PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The columns in the processed files are the following in order:  GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process PGCGROWTHCONDITIONS
Svi3_3_1_IPTG PGCGROWTHCONDITIONS
The cells for RNA extraction were immediately mixed with RNA Protect Bacterial reagent® (Qiagen) and processed by the RNAeasy Mini Kit (Qiagen) according to the manufacturers instructions. The cells for whole cell proteomics were chilled in ice-slush, pelleted at 14000 rpm, 4°C and the media was aspirated.  The cells were washed with 3×1.5 mL PBS with pelleting at as above in between. The final pellet was stored at -80°C until being shipped to the Proteomics Core Facility at University of Gothenburg for processing. The RNA was shipped to BGI for total RNA sequencing. PGCGROWTHCONDITIONS
The gene expression values were calculated as RPKM (reads per kilobase transcriptome per million mapped reads) by the inhouse BGI pipeline. PGCGROWTHCONDITIONS
The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
TruSeq PGCGROWTHCONDITIONS
BGI inhouse software “filter_fq” for basecalling and trimming PGCGROWTHCONDITIONS
Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol.  The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
E. coli MG1655 / Svi3-3 comp. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build:  NC_000913 PGCGROWTHCONDITIONS
Read-mapping was done with soap2.21. Mapping towards genes was done by the following parameters -m 0 -x 1000 -s 28 -l 32 -v 5 -r 2 -p 3 PGCGROWTHCONDITIONS
replicates: Svi3-3 replicate 1 / not induced PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The columns in the processed files are the following in order:  GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process PGCGROWTHCONDITIONS
Svi3_3_1 PGCGROWTHCONDITIONS
The cells for RNA extraction were immediately mixed with RNA Protect Bacterial reagent® (Qiagen) and processed by the RNAeasy Mini Kit (Qiagen) according to the manufacturers instructions. The cells for whole cell proteomics were chilled in ice-slush, pelleted at 14000 rpm, 4°C and the media was aspirated.  The cells were washed with 3×1.5 mL PBS with pelleting at as above in between. The final pellet was stored at -80°C until being shipped to the Proteomics Core Facility at University of Gothenburg for processing. The RNA was shipped to BGI for total RNA sequencing. PGCGROWTHCONDITIONS
The gene expression values were calculated as RPKM (reads per kilobase transcriptome per million mapped reads) by the inhouse BGI pipeline. PGCGROWTHCONDITIONS
The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
TruSeq PGCGROWTHCONDITIONS
BGI inhouse software “filter_fq” for basecalling and trimming PGCGROWTHCONDITIONS
Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol.  The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
E. coli MG1655 / Svi3-3 comp. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build:  NC_000913 PGCGROWTHCONDITIONS
induction: induced 50 µM IPTG PGCGROWTHCONDITIONS
Read-mapping was done with soap2.21. Mapping towards genes was done by the following parameters -m 0 -x 1000 -s 28 -l 32 -v 5 -r 2 -p 3 PGCGROWTHCONDITIONS
replicates: Svi3-3 replicate 2 / induced PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The columns in the processed files are the following in order:  GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process PGCGROWTHCONDITIONS
Svi3_3_2_IPTG PGCGROWTHCONDITIONS
The cells for RNA extraction were immediately mixed with RNA Protect Bacterial reagent® (Qiagen) and processed by the RNAeasy Mini Kit (Qiagen) according to the manufacturers instructions. The cells for whole cell proteomics were chilled in ice-slush, pelleted at 14000 rpm, 4°C and the media was aspirated.  The cells were washed with 3×1.5 mL PBS with pelleting at as above in between. The final pellet was stored at -80°C until being shipped to the Proteomics Core Facility at University of Gothenburg for processing. The RNA was shipped to BGI for total RNA sequencing. PGCGROWTHCONDITIONS
The gene expression values were calculated as RPKM (reads per kilobase transcriptome per million mapped reads) by the inhouse BGI pipeline. PGCGROWTHCONDITIONS
The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
TruSeq PGCGROWTHCONDITIONS
BGI inhouse software “filter_fq” for basecalling and trimming PGCGROWTHCONDITIONS
Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol.  The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
E. coli MG1655 / Svi3-3 comp. PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build:  NC_000913 PGCGROWTHCONDITIONS
Read-mapping was done with soap2.21. Mapping towards genes was done by the following parameters -m 0 -x 1000 -s 28 -l 32 -v 5 -r 2 -p 3 PGCGROWTHCONDITIONS
replicates: Svi3-3 replicate 2 / not induced PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The columns in the processed files are the following in order:  GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process PGCGROWTHCONDITIONS
Svi3_3_2 PGCGROWTHCONDITIONS
The cells for RNA extraction were immediately mixed with RNA Protect Bacterial reagent® (Qiagen) and processed by the RNAeasy Mini Kit (Qiagen) according to the manufacturers instructions. The cells for whole cell proteomics were chilled in ice-slush, pelleted at 14000 rpm, 4°C and the media was aspirated.  The cells were washed with 3×1.5 mL PBS with pelleting at as above in between. The final pellet was stored at -80°C until being shipped to the Proteomics Core Facility at University of Gothenburg for processing. The RNA was shipped to BGI for total RNA sequencing. PGCGROWTHCONDITIONS
The gene expression values were calculated as RPKM (reads per kilobase transcriptome per million mapped reads) by the inhouse BGI pipeline. PGCGROWTHCONDITIONS
The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
TruSeq PGCGROWTHCONDITIONS
BGI inhouse software “filter_fq” for basecalling and trimming PGCGROWTHCONDITIONS
Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol.  The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
E. coli MG1655 / pCA24N, -gfp PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build:  NC_000913 PGCGROWTHCONDITIONS
induction: induced 50 µM IPTG PGCGROWTHCONDITIONS
Read-mapping was done with soap2.21. Mapping towards genes was done by the following parameters -m 0 -x 1000 -s 28 -l 32 -v 5 -r 2 -p 3 PGCGROWTHCONDITIONS
replicates: WT replicate 1 / induced PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The columns in the processed files are the following in order:  GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process PGCGROWTHCONDITIONS
The cells for RNA extraction were immediately mixed with RNA Protect Bacterial reagent® (Qiagen) and processed by the RNAeasy Mini Kit (Qiagen) according to the manufacturers instructions. The cells for whole cell proteomics were chilled in ice-slush, pelleted at 14000 rpm, 4°C and the media was aspirated.  The cells were washed with 3×1.5 mL PBS with pelleting at as above in between. The final pellet was stored at -80°C until being shipped to the Proteomics Core Facility at University of Gothenburg for processing. The RNA was shipped to BGI for total RNA sequencing. PGCGROWTHCONDITIONS
The gene expression values were calculated as RPKM (reads per kilobase transcriptome per million mapped reads) by the inhouse BGI pipeline. PGCGROWTHCONDITIONS
The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
TruSeq PGCGROWTHCONDITIONS
WT1_IPTG PGCGROWTHCONDITIONS
BGI inhouse software “filter_fq” for basecalling and trimming PGCGROWTHCONDITIONS
Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol.  The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
E. coli MG1655 / pCA24N, -gfp PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
Genome_build:  NC_000913 PGCGROWTHCONDITIONS
induction: induced 50 µM IPTG PGCGROWTHCONDITIONS
Read-mapping was done with soap2.21. Mapping towards genes was done by the following parameters -m 0 -x 1000 -s 28 -l 32 -v 5 -r 2 -p 3 PGCGROWTHCONDITIONS
replicates: WT replicate 2 / induced PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The columns in the processed files are the following in order:  GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process PGCGROWTHCONDITIONS
The cells for RNA extraction were immediately mixed with RNA Protect Bacterial reagent® (Qiagen) and processed by the RNAeasy Mini Kit (Qiagen) according to the manufacturers instructions. The cells for whole cell proteomics were chilled in ice-slush, pelleted at 14000 rpm, 4°C and the media was aspirated.  The cells were washed with 3×1.5 mL PBS with pelleting at as above in between. The final pellet was stored at -80°C until being shipped to the Proteomics Core Facility at University of Gothenburg for processing. The RNA was shipped to BGI for total RNA sequencing. PGCGROWTHCONDITIONS
The gene expression values were calculated as RPKM (reads per kilobase transcriptome per million mapped reads) by the inhouse BGI pipeline. PGCGROWTHCONDITIONS
The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS
TruSeq PGCGROWTHCONDITIONS
WT2_IPTG PGCGROWTHCONDITIONS
An o/n culture of E. coli TolC was diluted to an OD600 of 0.1 and supplied with a final concentration of 0.5 µg/ml Carolacton in MeOH. Controls received the same volume MeOH. Three early time-points (t) were chosen to be analyzed by RNA-seq. Prior to addition of Carolacton (t0), t5, t15 and t30 min after addition of Carolacton. At each point, 5 ml of culture were mixed with an equal volume RNAprotect (Qiagen), incubated at room temperature (RT) for 5 min, the cells harvested by centrifugation, and the pellet frozen and stored at -80°C. PGCGROWTHCONDITIONS
E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS
Eco_TolC_0min_A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP018801 (https://www.ncbi.nlm.nih.gov/nuccore/CP018801) PGCGROWTHCONDITIONS
genotype: TolC defective (TolC-) PGCGROWTHCONDITIONS
Libraries of RNA fractions were constructed with the ScriptSeq V2 RNA-Seq Library Prep Kit (Illumina) according to the manufacturers guidelines. PGCGROWTHCONDITIONS
planktonic cells PGCGROWTHCONDITIONS
Raw read counts of transcripts were obtained by aligning samples 1-14 to the reference genome and counting mapped reads per feature using Rockhopper v2.0.3. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequences using FastQC v0.11.2. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The tab-delimited text files include raw read values for each time-point for both biol. replicates of control and Carolacton-treated samples as obtained from Rockhopper. A FASTA file on the series record contains the transcript sequences. PGCGROWTHCONDITIONS
time point (minutes): 0 PGCGROWTHCONDITIONS
Total cellular RNAs were extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturers protocol. Residual DNA in the fractions was digested by addition of 27 Kunitz units Dnase I (Qiagen), and absence of DNA verified by Polymerase chain reaction (PCR). mRNA enrichment was conducted using the Ribo-Zero kit for Gram-negative bacteria (epicentre). RNA quality control of the RNA extracts, as well as the successful mRNA enrichment, was conducted by using an Agilent 2100 Bioanalyzer. PGCGROWTHCONDITIONS
treatment: none PGCGROWTHCONDITIONS
An o/n culture of E. coli TolC was diluted to an OD600 of 0.1 and supplied with a final concentration of 0.5 µg/ml Carolacton in MeOH. Controls received the same volume MeOH. Three early time-points (t) were chosen to be analyzed by RNA-seq. Prior to addition of Carolacton (t0), t5, t15 and t30 min after addition of Carolacton. At each point, 5 ml of culture were mixed with an equal volume RNAprotect (Qiagen), incubated at room temperature (RT) for 5 min, the cells harvested by centrifugation, and the pellet frozen and stored at -80°C. PGCGROWTHCONDITIONS
E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS
Eco_TolC_0min_B PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP018801 (https://www.ncbi.nlm.nih.gov/nuccore/CP018801) PGCGROWTHCONDITIONS
genotype: TolC defective (TolC-) PGCGROWTHCONDITIONS
Libraries of RNA fractions were constructed with the ScriptSeq V2 RNA-Seq Library Prep Kit (Illumina) according to the manufacturers guidelines. PGCGROWTHCONDITIONS
planktonic cells PGCGROWTHCONDITIONS
Raw read counts of transcripts were obtained by aligning samples 1-14 to the reference genome and counting mapped reads per feature using Rockhopper v2.0.3. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequences using FastQC v0.11.2. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The tab-delimited text files include raw read values for each time-point for both biol. replicates of control and Carolacton-treated samples as obtained from Rockhopper. A FASTA file on the series record contains the transcript sequences. PGCGROWTHCONDITIONS
time point (minutes): 0 PGCGROWTHCONDITIONS
Total cellular RNAs were extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturers protocol. Residual DNA in the fractions was digested by addition of 27 Kunitz units Dnase I (Qiagen), and absence of DNA verified by Polymerase chain reaction (PCR). mRNA enrichment was conducted using the Ribo-Zero kit for Gram-negative bacteria (epicentre). RNA quality control of the RNA extracts, as well as the successful mRNA enrichment, was conducted by using an Agilent 2100 Bioanalyzer. PGCGROWTHCONDITIONS
treatment: none PGCGROWTHCONDITIONS
An o/n culture of E. coli TolC was diluted to an OD600 of 0.1 and supplied with a final concentration of 0.5 µg/ml Carolacton in MeOH. Controls received the same volume MeOH. Three early time-points (t) were chosen to be analyzed by RNA-seq. Prior to addition of Carolacton (t0), t5, t15 and t30 min after addition of Carolacton. At each point, 5 ml of culture were mixed with an equal volume RNAprotect (Qiagen), incubated at room temperature (RT) for 5 min, the cells harvested by centrifugation, and the pellet frozen and stored at -80°C. PGCGROWTHCONDITIONS
E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS
Eco_TolC_5min_control_A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP018801 (https://www.ncbi.nlm.nih.gov/nuccore/CP018801) PGCGROWTHCONDITIONS
genotype: TolC defective (TolC-) PGCGROWTHCONDITIONS
Libraries of RNA fractions were constructed with the ScriptSeq V2 RNA-Seq Library Prep Kit (Illumina) according to the manufacturers guidelines. PGCGROWTHCONDITIONS
planktonic cells PGCGROWTHCONDITIONS
Raw read counts of transcripts were obtained by aligning samples 1-14 to the reference genome and counting mapped reads per feature using Rockhopper v2.0.3. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequences using FastQC v0.11.2. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The tab-delimited text files include raw read values for each time-point for both biol. replicates of control and Carolacton-treated samples as obtained from Rockhopper. A FASTA file on the series record contains the transcript sequences. PGCGROWTHCONDITIONS
time point (minutes): 5 PGCGROWTHCONDITIONS
Total cellular RNAs were extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturers protocol. Residual DNA in the fractions was digested by addition of 27 Kunitz units Dnase I (Qiagen), and absence of DNA verified by Polymerase chain reaction (PCR). mRNA enrichment was conducted using the Ribo-Zero kit for Gram-negative bacteria (epicentre). RNA quality control of the RNA extracts, as well as the successful mRNA enrichment, was conducted by using an Agilent 2100 Bioanalyzer. PGCGROWTHCONDITIONS
treatment: none PGCGROWTHCONDITIONS
An o/n culture of E. coli TolC was diluted to an OD600 of 0.1 and supplied with a final concentration of 0.5 µg/ml Carolacton in MeOH. Controls received the same volume MeOH. Three early time-points (t) were chosen to be analyzed by RNA-seq. Prior to addition of Carolacton (t0), t5, t15 and t30 min after addition of Carolacton. At each point, 5 ml of culture were mixed with an equal volume RNAprotect (Qiagen), incubated at room temperature (RT) for 5 min, the cells harvested by centrifugation, and the pellet frozen and stored at -80°C. PGCGROWTHCONDITIONS
E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS
Eco_TolC_5min_control_B PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP018801 (https://www.ncbi.nlm.nih.gov/nuccore/CP018801) PGCGROWTHCONDITIONS
genotype: TolC defective (TolC-) PGCGROWTHCONDITIONS
Libraries of RNA fractions were constructed with the ScriptSeq V2 RNA-Seq Library Prep Kit (Illumina) according to the manufacturers guidelines. PGCGROWTHCONDITIONS
planktonic cells PGCGROWTHCONDITIONS
Raw read counts of transcripts were obtained by aligning samples 1-14 to the reference genome and counting mapped reads per feature using Rockhopper v2.0.3. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequences using FastQC v0.11.2. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The tab-delimited text files include raw read values for each time-point for both biol. replicates of control and Carolacton-treated samples as obtained from Rockhopper. A FASTA file on the series record contains the transcript sequences. PGCGROWTHCONDITIONS
time point (minutes): 5 PGCGROWTHCONDITIONS
Total cellular RNAs were extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturers protocol. Residual DNA in the fractions was digested by addition of 27 Kunitz units Dnase I (Qiagen), and absence of DNA verified by Polymerase chain reaction (PCR). mRNA enrichment was conducted using the Ribo-Zero kit for Gram-negative bacteria (epicentre). RNA quality control of the RNA extracts, as well as the successful mRNA enrichment, was conducted by using an Agilent 2100 Bioanalyzer. PGCGROWTHCONDITIONS
treatment: none PGCGROWTHCONDITIONS
An o/n culture of E. coli TolC was diluted to an OD600 of 0.1 and supplied with a final concentration of 0.5 µg/ml Carolacton in MeOH. Controls received the same volume MeOH. Three early time-points (t) were chosen to be analyzed by RNA-seq. Prior to addition of Carolacton (t0), t5, t15 and t30 min after addition of Carolacton. At each point, 5 ml of culture were mixed with an equal volume RNAprotect (Qiagen), incubated at room temperature (RT) for 5 min, the cells harvested by centrifugation, and the pellet frozen and stored at -80°C. PGCGROWTHCONDITIONS
E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS
Eco_TolC_5min_Carolacton_A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP018801 (https://www.ncbi.nlm.nih.gov/nuccore/CP018801) PGCGROWTHCONDITIONS
genotype: TolC defective (TolC-) PGCGROWTHCONDITIONS
Libraries of RNA fractions were constructed with the ScriptSeq V2 RNA-Seq Library Prep Kit (Illumina) according to the manufacturers guidelines. PGCGROWTHCONDITIONS
planktonic cells PGCGROWTHCONDITIONS
Raw read counts of transcripts were obtained by aligning samples 1-14 to the reference genome and counting mapped reads per feature using Rockhopper v2.0.3. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequences using FastQC v0.11.2. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The tab-delimited text files include raw read values for each time-point for both biol. replicates of control and Carolacton-treated samples as obtained from Rockhopper. A FASTA file on the series record contains the transcript sequences. PGCGROWTHCONDITIONS
time point (minutes): 5 PGCGROWTHCONDITIONS
Total cellular RNAs were extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturers protocol. Residual DNA in the fractions was digested by addition of 27 Kunitz units Dnase I (Qiagen), and absence of DNA verified by Polymerase chain reaction (PCR). mRNA enrichment was conducted using the Ribo-Zero kit for Gram-negative bacteria (epicentre). RNA quality control of the RNA extracts, as well as the successful mRNA enrichment, was conducted by using an Agilent 2100 Bioanalyzer. PGCGROWTHCONDITIONS
treatment: 0.5 µg/ml Carolacton PGCGROWTHCONDITIONS
An o/n culture of E. coli TolC was diluted to an OD600 of 0.1 and supplied with a final concentration of 0.5 µg/ml Carolacton in MeOH. Controls received the same volume MeOH. Three early time-points (t) were chosen to be analyzed by RNA-seq. Prior to addition of Carolacton (t0), t5, t15 and t30 min after addition of Carolacton. At each point, 5 ml of culture were mixed with an equal volume RNAprotect (Qiagen), incubated at room temperature (RT) for 5 min, the cells harvested by centrifugation, and the pellet frozen and stored at -80°C. PGCGROWTHCONDITIONS
E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS
Eco_TolC_5min_Carolacton_B PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP018801 (https://www.ncbi.nlm.nih.gov/nuccore/CP018801) PGCGROWTHCONDITIONS
genotype: TolC defective (TolC-) PGCGROWTHCONDITIONS
Libraries of RNA fractions were constructed with the ScriptSeq V2 RNA-Seq Library Prep Kit (Illumina) according to the manufacturers guidelines. PGCGROWTHCONDITIONS
planktonic cells PGCGROWTHCONDITIONS
Raw read counts of transcripts were obtained by aligning samples 1-14 to the reference genome and counting mapped reads per feature using Rockhopper v2.0.3. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequences using FastQC v0.11.2. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The tab-delimited text files include raw read values for each time-point for both biol. replicates of control and Carolacton-treated samples as obtained from Rockhopper. A FASTA file on the series record contains the transcript sequences. PGCGROWTHCONDITIONS
time point (minutes): 5 PGCGROWTHCONDITIONS
Total cellular RNAs were extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturers protocol. Residual DNA in the fractions was digested by addition of 27 Kunitz units Dnase I (Qiagen), and absence of DNA verified by Polymerase chain reaction (PCR). mRNA enrichment was conducted using the Ribo-Zero kit for Gram-negative bacteria (epicentre). RNA quality control of the RNA extracts, as well as the successful mRNA enrichment, was conducted by using an Agilent 2100 Bioanalyzer. PGCGROWTHCONDITIONS
treatment: 0.5 µg/ml Carolacton PGCGROWTHCONDITIONS
An o/n culture of E. coli TolC was diluted to an OD600 of 0.1 and supplied with a final concentration of 0.5 µg/ml Carolacton in MeOH. Controls received the same volume MeOH. Three early time-points (t) were chosen to be analyzed by RNA-seq. Prior to addition of Carolacton (t0), t5, t15 and t30 min after addition of Carolacton. At each point, 5 ml of culture were mixed with an equal volume RNAprotect (Qiagen), incubated at room temperature (RT) for 5 min, the cells harvested by centrifugation, and the pellet frozen and stored at -80°C. PGCGROWTHCONDITIONS
E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS
Eco_TolC_15min_control_A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP018801 (https://www.ncbi.nlm.nih.gov/nuccore/CP018801) PGCGROWTHCONDITIONS
genotype: TolC defective (TolC-) PGCGROWTHCONDITIONS
Libraries of RNA fractions were constructed with the ScriptSeq V2 RNA-Seq Library Prep Kit (Illumina) according to the manufacturers guidelines. PGCGROWTHCONDITIONS
planktonic cells PGCGROWTHCONDITIONS
Raw read counts of transcripts were obtained by aligning samples 1-14 to the reference genome and counting mapped reads per feature using Rockhopper v2.0.3. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequences using FastQC v0.11.2. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The tab-delimited text files include raw read values for each time-point for both biol. replicates of control and Carolacton-treated samples as obtained from Rockhopper. A FASTA file on the series record contains the transcript sequences. PGCGROWTHCONDITIONS
time point (minutes): 15 PGCGROWTHCONDITIONS
Total cellular RNAs were extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturers protocol. Residual DNA in the fractions was digested by addition of 27 Kunitz units Dnase I (Qiagen), and absence of DNA verified by Polymerase chain reaction (PCR). mRNA enrichment was conducted using the Ribo-Zero kit for Gram-negative bacteria (epicentre). RNA quality control of the RNA extracts, as well as the successful mRNA enrichment, was conducted by using an Agilent 2100 Bioanalyzer. PGCGROWTHCONDITIONS
treatment: none PGCGROWTHCONDITIONS
An o/n culture of E. coli TolC was diluted to an OD600 of 0.1 and supplied with a final concentration of 0.5 µg/ml Carolacton in MeOH. Controls received the same volume MeOH. Three early time-points (t) were chosen to be analyzed by RNA-seq. Prior to addition of Carolacton (t0), t5, t15 and t30 min after addition of Carolacton. At each point, 5 ml of culture were mixed with an equal volume RNAprotect (Qiagen), incubated at room temperature (RT) for 5 min, the cells harvested by centrifugation, and the pellet frozen and stored at -80°C. PGCGROWTHCONDITIONS
E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS
Eco_TolC_15min_control_B PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP018801 (https://www.ncbi.nlm.nih.gov/nuccore/CP018801) PGCGROWTHCONDITIONS
genotype: TolC defective (TolC-) PGCGROWTHCONDITIONS
Libraries of RNA fractions were constructed with the ScriptSeq V2 RNA-Seq Library Prep Kit (Illumina) according to the manufacturers guidelines. PGCGROWTHCONDITIONS
planktonic cells PGCGROWTHCONDITIONS
Raw read counts of transcripts were obtained by aligning samples 1-14 to the reference genome and counting mapped reads per feature using Rockhopper v2.0.3. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequences using FastQC v0.11.2. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The tab-delimited text files include raw read values for each time-point for both biol. replicates of control and Carolacton-treated samples as obtained from Rockhopper. A FASTA file on the series record contains the transcript sequences. PGCGROWTHCONDITIONS
time point (minutes): 15 PGCGROWTHCONDITIONS
Total cellular RNAs were extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturers protocol. Residual DNA in the fractions was digested by addition of 27 Kunitz units Dnase I (Qiagen), and absence of DNA verified by Polymerase chain reaction (PCR). mRNA enrichment was conducted using the Ribo-Zero kit for Gram-negative bacteria (epicentre). RNA quality control of the RNA extracts, as well as the successful mRNA enrichment, was conducted by using an Agilent 2100 Bioanalyzer. PGCGROWTHCONDITIONS
treatment: none PGCGROWTHCONDITIONS
An o/n culture of E. coli TolC was diluted to an OD600 of 0.1 and supplied with a final concentration of 0.5 µg/ml Carolacton in MeOH. Controls received the same volume MeOH. Three early time-points (t) were chosen to be analyzed by RNA-seq. Prior to addition of Carolacton (t0), t5, t15 and t30 min after addition of Carolacton. At each point, 5 ml of culture were mixed with an equal volume RNAprotect (Qiagen), incubated at room temperature (RT) for 5 min, the cells harvested by centrifugation, and the pellet frozen and stored at -80°C. PGCGROWTHCONDITIONS
E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS
Eco_TolC_15min_Carolacton_A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP018801 (https://www.ncbi.nlm.nih.gov/nuccore/CP018801) PGCGROWTHCONDITIONS
genotype: TolC defective (TolC-) PGCGROWTHCONDITIONS
Libraries of RNA fractions were constructed with the ScriptSeq V2 RNA-Seq Library Prep Kit (Illumina) according to the manufacturers guidelines. PGCGROWTHCONDITIONS
planktonic cells PGCGROWTHCONDITIONS
Raw read counts of transcripts were obtained by aligning samples 1-14 to the reference genome and counting mapped reads per feature using Rockhopper v2.0.3. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequences using FastQC v0.11.2. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The tab-delimited text files include raw read values for each time-point for both biol. replicates of control and Carolacton-treated samples as obtained from Rockhopper. A FASTA file on the series record contains the transcript sequences. PGCGROWTHCONDITIONS
time point (minutes): 15 PGCGROWTHCONDITIONS
Total cellular RNAs were extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturers protocol. Residual DNA in the fractions was digested by addition of 27 Kunitz units Dnase I (Qiagen), and absence of DNA verified by Polymerase chain reaction (PCR). mRNA enrichment was conducted using the Ribo-Zero kit for Gram-negative bacteria (epicentre). RNA quality control of the RNA extracts, as well as the successful mRNA enrichment, was conducted by using an Agilent 2100 Bioanalyzer. PGCGROWTHCONDITIONS
treatment: 0.5 µg/ml Carolacton PGCGROWTHCONDITIONS
An o/n culture of E. coli TolC was diluted to an OD600 of 0.1 and supplied with a final concentration of 0.5 µg/ml Carolacton in MeOH. Controls received the same volume MeOH. Three early time-points (t) were chosen to be analyzed by RNA-seq. Prior to addition of Carolacton (t0), t5, t15 and t30 min after addition of Carolacton. At each point, 5 ml of culture were mixed with an equal volume RNAprotect (Qiagen), incubated at room temperature (RT) for 5 min, the cells harvested by centrifugation, and the pellet frozen and stored at -80°C. PGCGROWTHCONDITIONS
E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS
Eco_TolC_15min_Carolacton_B PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP018801 (https://www.ncbi.nlm.nih.gov/nuccore/CP018801) PGCGROWTHCONDITIONS
genotype: TolC defective (TolC-) PGCGROWTHCONDITIONS
Libraries of RNA fractions were constructed with the ScriptSeq V2 RNA-Seq Library Prep Kit (Illumina) according to the manufacturers guidelines. PGCGROWTHCONDITIONS
planktonic cells PGCGROWTHCONDITIONS
Raw read counts of transcripts were obtained by aligning samples 1-14 to the reference genome and counting mapped reads per feature using Rockhopper v2.0.3. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequences using FastQC v0.11.2. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The tab-delimited text files include raw read values for each time-point for both biol. replicates of control and Carolacton-treated samples as obtained from Rockhopper. A FASTA file on the series record contains the transcript sequences. PGCGROWTHCONDITIONS
time point (minutes): 15 PGCGROWTHCONDITIONS
Total cellular RNAs were extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturers protocol. Residual DNA in the fractions was digested by addition of 27 Kunitz units Dnase I (Qiagen), and absence of DNA verified by Polymerase chain reaction (PCR). mRNA enrichment was conducted using the Ribo-Zero kit for Gram-negative bacteria (epicentre). RNA quality control of the RNA extracts, as well as the successful mRNA enrichment, was conducted by using an Agilent 2100 Bioanalyzer. PGCGROWTHCONDITIONS
treatment: 0.5 µg/ml Carolacton PGCGROWTHCONDITIONS
An o/n culture of E. coli TolC was diluted to an OD600 of 0.1 and supplied with a final concentration of 0.5 µg/ml Carolacton in MeOH. Controls received the same volume MeOH. Three early time-points (t) were chosen to be analyzed by RNA-seq. Prior to addition of Carolacton (t0), t5, t15 and t30 min after addition of Carolacton. At each point, 5 ml of culture were mixed with an equal volume RNAprotect (Qiagen), incubated at room temperature (RT) for 5 min, the cells harvested by centrifugation, and the pellet frozen and stored at -80°C. PGCGROWTHCONDITIONS
E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS
Eco_TolC_30min_control_A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP018801 (https://www.ncbi.nlm.nih.gov/nuccore/CP018801) PGCGROWTHCONDITIONS
genotype: TolC defective (TolC-) PGCGROWTHCONDITIONS
Libraries of RNA fractions were constructed with the ScriptSeq V2 RNA-Seq Library Prep Kit (Illumina) according to the manufacturers guidelines. PGCGROWTHCONDITIONS
planktonic cells PGCGROWTHCONDITIONS
Raw read counts of transcripts were obtained by aligning samples 1-14 to the reference genome and counting mapped reads per feature using Rockhopper v2.0.3. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequences using FastQC v0.11.2. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The tab-delimited text files include raw read values for each time-point for both biol. replicates of control and Carolacton-treated samples as obtained from Rockhopper. A FASTA file on the series record contains the transcript sequences. PGCGROWTHCONDITIONS
time point (minutes): 30 PGCGROWTHCONDITIONS
Total cellular RNAs were extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturers protocol. Residual DNA in the fractions was digested by addition of 27 Kunitz units Dnase I (Qiagen), and absence of DNA verified by Polymerase chain reaction (PCR). mRNA enrichment was conducted using the Ribo-Zero kit for Gram-negative bacteria (epicentre). RNA quality control of the RNA extracts, as well as the successful mRNA enrichment, was conducted by using an Agilent 2100 Bioanalyzer. PGCGROWTHCONDITIONS
treatment: none PGCGROWTHCONDITIONS
An o/n culture of E. coli TolC was diluted to an OD600 of 0.1 and supplied with a final concentration of 0.5 µg/ml Carolacton in MeOH. Controls received the same volume MeOH. Three early time-points (t) were chosen to be analyzed by RNA-seq. Prior to addition of Carolacton (t0), t5, t15 and t30 min after addition of Carolacton. At each point, 5 ml of culture were mixed with an equal volume RNAprotect (Qiagen), incubated at room temperature (RT) for 5 min, the cells harvested by centrifugation, and the pellet frozen and stored at -80°C. PGCGROWTHCONDITIONS
E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS
Eco_TolC_30min_control_B PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP018801 (https://www.ncbi.nlm.nih.gov/nuccore/CP018801) PGCGROWTHCONDITIONS
genotype: TolC defective (TolC-) PGCGROWTHCONDITIONS
Libraries of RNA fractions were constructed with the ScriptSeq V2 RNA-Seq Library Prep Kit (Illumina) according to the manufacturers guidelines. PGCGROWTHCONDITIONS
planktonic cells PGCGROWTHCONDITIONS
Raw read counts of transcripts were obtained by aligning samples 1-14 to the reference genome and counting mapped reads per feature using Rockhopper v2.0.3. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequences using FastQC v0.11.2. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The tab-delimited text files include raw read values for each time-point for both biol. replicates of control and Carolacton-treated samples as obtained from Rockhopper. A FASTA file on the series record contains the transcript sequences. PGCGROWTHCONDITIONS
time point (minutes): 30 PGCGROWTHCONDITIONS
Total cellular RNAs were extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturers protocol. Residual DNA in the fractions was digested by addition of 27 Kunitz units Dnase I (Qiagen), and absence of DNA verified by Polymerase chain reaction (PCR). mRNA enrichment was conducted using the Ribo-Zero kit for Gram-negative bacteria (epicentre). RNA quality control of the RNA extracts, as well as the successful mRNA enrichment, was conducted by using an Agilent 2100 Bioanalyzer. PGCGROWTHCONDITIONS
treatment: none PGCGROWTHCONDITIONS
An o/n culture of E. coli TolC was diluted to an OD600 of 0.1 and supplied with a final concentration of 0.5 µg/ml Carolacton in MeOH. Controls received the same volume MeOH. Three early time-points (t) were chosen to be analyzed by RNA-seq. Prior to addition of Carolacton (t0), t5, t15 and t30 min after addition of Carolacton. At each point, 5 ml of culture were mixed with an equal volume RNAprotect (Qiagen), incubated at room temperature (RT) for 5 min, the cells harvested by centrifugation, and the pellet frozen and stored at -80°C. PGCGROWTHCONDITIONS
E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS
Eco_TolC_30min_Carolacton_A PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP018801 (https://www.ncbi.nlm.nih.gov/nuccore/CP018801) PGCGROWTHCONDITIONS
genotype: TolC defective (TolC-) PGCGROWTHCONDITIONS
Libraries of RNA fractions were constructed with the ScriptSeq V2 RNA-Seq Library Prep Kit (Illumina) according to the manufacturers guidelines. PGCGROWTHCONDITIONS
planktonic cells PGCGROWTHCONDITIONS
Raw read counts of transcripts were obtained by aligning samples 1-14 to the reference genome and counting mapped reads per feature using Rockhopper v2.0.3. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequences using FastQC v0.11.2. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The tab-delimited text files include raw read values for each time-point for both biol. replicates of control and Carolacton-treated samples as obtained from Rockhopper. A FASTA file on the series record contains the transcript sequences. PGCGROWTHCONDITIONS
time point (minutes): 30 PGCGROWTHCONDITIONS
Total cellular RNAs were extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturers protocol. Residual DNA in the fractions was digested by addition of 27 Kunitz units Dnase I (Qiagen), and absence of DNA verified by Polymerase chain reaction (PCR). mRNA enrichment was conducted using the Ribo-Zero kit for Gram-negative bacteria (epicentre). RNA quality control of the RNA extracts, as well as the successful mRNA enrichment, was conducted by using an Agilent 2100 Bioanalyzer. PGCGROWTHCONDITIONS
treatment: 0.5 µg/ml Carolacton PGCGROWTHCONDITIONS
An o/n culture of E. coli TolC was diluted to an OD600 of 0.1 and supplied with a final concentration of 0.5 µg/ml Carolacton in MeOH. Controls received the same volume MeOH. Three early time-points (t) were chosen to be analyzed by RNA-seq. Prior to addition of Carolacton (t0), t5, t15 and t30 min after addition of Carolacton. At each point, 5 ml of culture were mixed with an equal volume RNAprotect (Qiagen), incubated at room temperature (RT) for 5 min, the cells harvested by centrifugation, and the pellet frozen and stored at -80°C. PGCGROWTHCONDITIONS
E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS
Eco_TolC_30min_Carolacton_B PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP018801 (https://www.ncbi.nlm.nih.gov/nuccore/CP018801) PGCGROWTHCONDITIONS
genotype: TolC defective (TolC-) PGCGROWTHCONDITIONS
Libraries of RNA fractions were constructed with the ScriptSeq V2 RNA-Seq Library Prep Kit (Illumina) according to the manufacturers guidelines. PGCGROWTHCONDITIONS
planktonic cells PGCGROWTHCONDITIONS
Raw read counts of transcripts were obtained by aligning samples 1-14 to the reference genome and counting mapped reads per feature using Rockhopper v2.0.3. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequences using FastQC v0.11.2. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: The tab-delimited text files include raw read values for each time-point for both biol. replicates of control and Carolacton-treated samples as obtained from Rockhopper. A FASTA file on the series record contains the transcript sequences. PGCGROWTHCONDITIONS
time point (minutes): 30 PGCGROWTHCONDITIONS
Total cellular RNAs were extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturers protocol. Residual DNA in the fractions was digested by addition of 27 Kunitz units Dnase I (Qiagen), and absence of DNA verified by Polymerase chain reaction (PCR). mRNA enrichment was conducted using the Ribo-Zero kit for Gram-negative bacteria (epicentre). RNA quality control of the RNA extracts, as well as the successful mRNA enrichment, was conducted by using an Agilent 2100 Bioanalyzer. PGCGROWTHCONDITIONS
treatment: 0.5 µg/ml Carolacton PGCGROWTHCONDITIONS
ATCC2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
first strand cDNA was performed by the use of SuperScriptII and the second strand cDNA synthesis was done before end-pair and dA-tailing PGCGROWTHCONDITIONS
Following \TruSeq RNA Sample Preparation Guide\. PGCGROWTHCONDITIONS
Genome_build: UCSC mm10 PGCGROWTHCONDITIONS
Human PGCGROWTHCONDITIONS
No treatment PGCGROWTHCONDITIONS
Reads longer than 25 nt and ≤ 2 N (ambiguous nucleotides) were preserved. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-Seq of E. coli were done using blind and fit-only parameter in DE-Seq pakage PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8 PGCGROWTHCONDITIONS
strain: E. coli ATCC 25922 PGCGROWTHCONDITIONS
Strains were harvested in MH broth at log phase PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample PGCGROWTHCONDITIONS
Total RNAs were extracted from the bacterial isolates using TRIzol PGCGROWTHCONDITIONS
Using blind and fit-only parameter in DE-Seq pakage, expressions of genes in all samples were changed to count per gene, using RNA-Seq protocol on Illumina HiSeq2500 platform PGCGROWTHCONDITIONS
ATCC3 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
first strand cDNA was performed by the use of SuperScriptII and the second strand cDNA synthesis was done before end-pair and dA-tailing PGCGROWTHCONDITIONS
Following \TruSeq RNA Sample Preparation Guide\. PGCGROWTHCONDITIONS
Genome_build: UCSC mm10 PGCGROWTHCONDITIONS
Human PGCGROWTHCONDITIONS
No treatment PGCGROWTHCONDITIONS
Reads longer than 25 nt and ≤ 2 N (ambiguous nucleotides) were preserved. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-Seq of E. coli were done using blind and fit-only parameter in DE-Seq pakage PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8 PGCGROWTHCONDITIONS
strain: E. coli ATCC 25922 PGCGROWTHCONDITIONS
Strains were harvested in MH broth at log phase PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample PGCGROWTHCONDITIONS
Total RNAs were extracted from the bacterial isolates using TRIzol PGCGROWTHCONDITIONS
Using blind and fit-only parameter in DE-Seq pakage, expressions of genes in all samples were changed to count per gene, using RNA-Seq protocol on Illumina HiSeq2500 platform PGCGROWTHCONDITIONS
Broiler Fecal PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
first strand cDNA was performed by the use of SuperScriptII and the second strand cDNA synthesis was done before end-pair and dA-tailing PGCGROWTHCONDITIONS
Following \TruSeq RNA Sample Preparation Guide\. PGCGROWTHCONDITIONS
Genome_build: UCSC mm10 PGCGROWTHCONDITIONS
No treatment PGCGROWTHCONDITIONS
Reads longer than 25 nt and ≤ 2 N (ambiguous nucleotides) were preserved. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-Seq of E. coli were done using blind and fit-only parameter in DE-Seq pakage PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8 PGCGROWTHCONDITIONS
sp1 PGCGROWTHCONDITIONS
strain: Poultry E. coli Virulent and multidrug resistant PGCGROWTHCONDITIONS
Strains were harvested in MH broth at log phase PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample PGCGROWTHCONDITIONS
Total RNAs were extracted from the bacterial isolates using TRIzol PGCGROWTHCONDITIONS
Using blind and fit-only parameter in DE-Seq pakage, expressions of genes in all samples were changed to count per gene, using RNA-Seq protocol on Illumina HiSeq2500 platform PGCGROWTHCONDITIONS
Broiler Fecal PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
first strand cDNA was performed by the use of SuperScriptII and the second strand cDNA synthesis was done before end-pair and dA-tailing PGCGROWTHCONDITIONS
Following \TruSeq RNA Sample Preparation Guide\. PGCGROWTHCONDITIONS
Genome_build: UCSC mm10 PGCGROWTHCONDITIONS
No treatment PGCGROWTHCONDITIONS
Reads longer than 25 nt and ≤ 2 N (ambiguous nucleotides) were preserved. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA-Seq of E. coli were done using blind and fit-only parameter in DE-Seq pakage PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8 PGCGROWTHCONDITIONS
sp2 PGCGROWTHCONDITIONS
strain: Poultry E. coli Virulent and multidrug resistant PGCGROWTHCONDITIONS
Strains were harvested in MH broth at log phase PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample PGCGROWTHCONDITIONS
Total RNAs were extracted from the bacterial isolates using TRIzol PGCGROWTHCONDITIONS
Using blind and fit-only parameter in DE-Seq pakage, expressions of genes in all samples were changed to count per gene, using RNA-Seq protocol on Illumina HiSeq2500 platform PGCGROWTHCONDITIONS
biomass collected in the transition between exponential to stationary phase PGCGROWTHCONDITIONS
EHEC in LB Experiment 1 [RNA-Seq] PGCGROWTHCONDITIONS
Escherichia coli O157:H7 str. EDL933 PGCGROWTHCONDITIONS
Genome_build: NC_002655 PGCGROWTHCONDITIONS
growth media: LB medium PGCGROWTHCONDITIONS
Illumina fastq files were submitted to the galaxy pipeline => grooming => mapping to NC_002655 using bowtie2 (default but seed 19 nt & zero mismatches within seed) PGCGROWTHCONDITIONS
LB medium, 180 rpm shaking, at 37°C, between exponential and stationary phase PGCGROWTHCONDITIONS
ligation, rt-PCR, PCR PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Reads, RPKM, and RCV mapped to NC_002655 (RCV = Ribosomal Coverage Value = RPKM-footprint over RPKM-transcription) PGCGROWTHCONDITIONS
Trizol for RNAseq, gradient centrifugation => RNase digestions => Trizol => gel extraction for RIBOseq PGCGROWTHCONDITIONS
Truseq Small RNA PGCGROWTHCONDITIONS
biomass collected in the transition between exponential to stationary phase PGCGROWTHCONDITIONS
EHEC in LB Experiment 2 [RNA-Seq] PGCGROWTHCONDITIONS
Escherichia coli O157:H7 str. EDL933 PGCGROWTHCONDITIONS
Genome_build: NC_002655 PGCGROWTHCONDITIONS
growth media: LB medium PGCGROWTHCONDITIONS
Illumina fastq files were submitted to the galaxy pipeline => grooming => mapping to NC_002655 using bowtie2 (default but seed 19 nt & zero mismatches within seed) PGCGROWTHCONDITIONS
LB medium, 180 rpm shaking, at 37°C, between exponential and stationary phase PGCGROWTHCONDITIONS
ligation, rt-PCR, PCR PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Reads, RPKM, and RCV mapped to NC_002655 (RCV = Ribosomal Coverage Value = RPKM-footprint over RPKM-transcription) PGCGROWTHCONDITIONS
Trizol for RNAseq, gradient centrifugation => RNase digestions => Trizol => gel extraction for RIBOseq PGCGROWTHCONDITIONS
Truseq Small RNA PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_018220 and NC_000913 PGCGROWTHCONDITIONS
MG1655_LB1 PGCGROWTHCONDITIONS
MG1655_LB PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Single colonies of P. putida strain DOT-T1E and E. coli MG1655 were grown overnight in Luria–Bertani (LB) medium at 30°C. Overnight cultures were diluted to a starting OD600 of 0.01 in the same medium and 50 ml aliquots were disposed in separate 250 ml Erlenmeyer flasks and incubated with shaking at 200 rpm. When cultures reached exponential phase (0.5 at OD600), antibiotics were added at sub-lethal concentrations to the culture medium to reach a final concentration of 1 µg/ml kanamycin, 300 µg/ml ampicillin, 150 µg/ml chloramphenicol, 4 µg/ml tetracycline, 0.5 µg/ml ciprofloxacin, 300 µg/ml spectinomycin, 500 µg/ml rifampicin and 2 µg/ml gentamicin. Then cultures were incubated under the same conditions for one hour more. Cells were harvested by centrifugation at 8000 g for 10 min and suspended immediately in stop solution (95% (v/v) ethanol, 5% (v/v) phenol) and pelleted by centrifugation. After that, total RNA was extracted with Trizol (Invitrogen). Removal of DNA was carried out by treatment with DNase I (Fermentas) in combination with the RNase inhibitor RiboLock (Fermentas). The integrity and quality of total RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies). PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CoK12_LB.xlsx: Average expression values of reads related with MG1655 strain in samples Co-culture_LB1 and LB2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CoT1E_LB.xlsx: Average expression values of reads related with DOT-T1E strain in samples Co-culture_LB1 and LB2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: K12_LB.xlsx: Average of expression values of samples MG1655_LB1 and LB2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: T1E_LB.xlsx: Average of expression values of samples DOT-T1E_LB1 and LB2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include the average of the expression values obtained in Rockhopper for the replicates of each condition PGCGROWTHCONDITIONS
We use Rockhopper for alignment and the complete analysis of data PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_018220 and NC_000913 PGCGROWTHCONDITIONS
MG1655_LB2 PGCGROWTHCONDITIONS
MG1655_LB PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Single colonies of P. putida strain DOT-T1E and E. coli MG1655 were grown overnight in Luria–Bertani (LB) medium at 30°C. Overnight cultures were diluted to a starting OD600 of 0.01 in the same medium and 50 ml aliquots were disposed in separate 250 ml Erlenmeyer flasks and incubated with shaking at 200 rpm. When cultures reached exponential phase (0.5 at OD600), antibiotics were added at sub-lethal concentrations to the culture medium to reach a final concentration of 1 µg/ml kanamycin, 300 µg/ml ampicillin, 150 µg/ml chloramphenicol, 4 µg/ml tetracycline, 0.5 µg/ml ciprofloxacin, 300 µg/ml spectinomycin, 500 µg/ml rifampicin and 2 µg/ml gentamicin. Then cultures were incubated under the same conditions for one hour more. Cells were harvested by centrifugation at 8000 g for 10 min and suspended immediately in stop solution (95% (v/v) ethanol, 5% (v/v) phenol) and pelleted by centrifugation. After that, total RNA was extracted with Trizol (Invitrogen). Removal of DNA was carried out by treatment with DNase I (Fermentas) in combination with the RNase inhibitor RiboLock (Fermentas). The integrity and quality of total RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies). PGCGROWTHCONDITIONS
strain: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CoK12_LB.xlsx: Average expression values of reads related with MG1655 strain in samples Co-culture_LB1 and LB2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CoT1E_LB.xlsx: Average expression values of reads related with DOT-T1E strain in samples Co-culture_LB1 and LB2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: K12_LB.xlsx: Average of expression values of samples MG1655_LB1 and LB2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: T1E_LB.xlsx: Average of expression values of samples DOT-T1E_LB1 and LB2 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimited text files include the average of the expression values obtained in Rockhopper for the replicates of each condition PGCGROWTHCONDITIONS
We use Rockhopper for alignment and the complete analysis of data PGCGROWTHCONDITIONS
Adapters trimmed with Cutadapt (v1.12) PGCGROWTHCONDITIONS
Aligned to NC_000913.3 with bwa version 0.7.7 PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
Cells were grown to exponential phase in Lysogeny broth, 37oC with shaking PGCGROWTHCONDITIONS
Cells were harvested after the addition of rifampicin  (250 μg/ml) to stop nascent transcription and quenched with stop solution (10% phenol in ethanol). The first timepoint was taken 3.5 minutes after addition of the antibiotic to give time for the diffusion of rifampicin into the cells and binding of the antibiotic to RNA polymerase. This sample was called 0 minutes, and further samples were taken at 2.5, 5, 7.5, 10, and 20 minutes from wild-type E. coli and the RNase III mutant. A partial biological replicate of wild-type was taken (0, 2.5, and 7.5 minutes), to examine the reproducibility between samples. PGCGROWTHCONDITIONS
Count reads aligned to each base IGVtools (version 2.3.71), window size = 1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gave a pseudocount of 0.01 to all values of 0 PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
Index and sort alignments with samtools version 1.2 PGCGROWTHCONDITIONS
Normalized decay values with average of stable genes ssrA, ssrS, and rnpB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA reduction with EpiCentre Ribo-Zero Gram Negative Ribosomal RNA reduction kit (2.5ug) & TruSeq RNA Library Prep PGCGROWTHCONDITIONS
strain: MG1693 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS
time point: time0 PGCGROWTHCONDITIONS
Total RNA was extracted and DNase-treated according to published protocols (Khodurksy A, Bernstein J, Peter B, Rhodius V, Wendisch V, Zimmer D. Escherichia coli Spotted Double-Strand DNA Microarrays) PGCGROWTHCONDITIONS
WTA_time0 PGCGROWTHCONDITIONS
Adapters trimmed with Cutadapt (v1.12) PGCGROWTHCONDITIONS
Aligned to NC_000913.3 with bwa version 0.7.7 PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
Cells were grown to exponential phase in Lysogeny broth, 37oC with shaking PGCGROWTHCONDITIONS
Cells were harvested after the addition of rifampicin  (250 μg/ml) to stop nascent transcription and quenched with stop solution (10% phenol in ethanol). The first timepoint was taken 3.5 minutes after addition of the antibiotic to give time for the diffusion of rifampicin into the cells and binding of the antibiotic to RNA polymerase. This sample was called 0 minutes, and further samples were taken at 2.5, 5, 7.5, 10, and 20 minutes from wild-type E. coli and the RNase III mutant. A partial biological replicate of wild-type was taken (0, 2.5, and 7.5 minutes), to examine the reproducibility between samples. PGCGROWTHCONDITIONS
Count reads aligned to each base IGVtools (version 2.3.71), window size = 1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gave a pseudocount of 0.01 to all values of 0 PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
Index and sort alignments with samtools version 1.2 PGCGROWTHCONDITIONS
Normalized decay values with average of stable genes ssrA, ssrS, and rnpB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA reduction with EpiCentre Ribo-Zero Gram Negative Ribosomal RNA reduction kit (2.5ug) & TruSeq RNA Library Prep PGCGROWTHCONDITIONS
strain: MG1693 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS
time point: time2.5 PGCGROWTHCONDITIONS
Total RNA was extracted and DNase-treated according to published protocols (Khodurksy A, Bernstein J, Peter B, Rhodius V, Wendisch V, Zimmer D. Escherichia coli Spotted Double-Strand DNA Microarrays) PGCGROWTHCONDITIONS
WTA_time2.5 PGCGROWTHCONDITIONS
Adapters trimmed with Cutadapt (v1.12) PGCGROWTHCONDITIONS
Aligned to NC_000913.3 with bwa version 0.7.7 PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
Cells were grown to exponential phase in Lysogeny broth, 37oC with shaking PGCGROWTHCONDITIONS
Cells were harvested after the addition of rifampicin  (250 μg/ml) to stop nascent transcription and quenched with stop solution (10% phenol in ethanol). The first timepoint was taken 3.5 minutes after addition of the antibiotic to give time for the diffusion of rifampicin into the cells and binding of the antibiotic to RNA polymerase. This sample was called 0 minutes, and further samples were taken at 2.5, 5, 7.5, 10, and 20 minutes from wild-type E. coli and the RNase III mutant. A partial biological replicate of wild-type was taken (0, 2.5, and 7.5 minutes), to examine the reproducibility between samples. PGCGROWTHCONDITIONS
Count reads aligned to each base IGVtools (version 2.3.71), window size = 1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gave a pseudocount of 0.01 to all values of 0 PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
Index and sort alignments with samtools version 1.2 PGCGROWTHCONDITIONS
Normalized decay values with average of stable genes ssrA, ssrS, and rnpB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA reduction with EpiCentre Ribo-Zero Gram Negative Ribosomal RNA reduction kit (2.5ug) & TruSeq RNA Library Prep PGCGROWTHCONDITIONS
strain: MG1693 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS
time point: time5 PGCGROWTHCONDITIONS
Total RNA was extracted and DNase-treated according to published protocols (Khodurksy A, Bernstein J, Peter B, Rhodius V, Wendisch V, Zimmer D. Escherichia coli Spotted Double-Strand DNA Microarrays) PGCGROWTHCONDITIONS
WTA_time5 PGCGROWTHCONDITIONS
Adapters trimmed with Cutadapt (v1.12) PGCGROWTHCONDITIONS
Aligned to NC_000913.3 with bwa version 0.7.7 PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
Cells were grown to exponential phase in Lysogeny broth, 37oC with shaking PGCGROWTHCONDITIONS
Cells were harvested after the addition of rifampicin  (250 μg/ml) to stop nascent transcription and quenched with stop solution (10% phenol in ethanol). The first timepoint was taken 3.5 minutes after addition of the antibiotic to give time for the diffusion of rifampicin into the cells and binding of the antibiotic to RNA polymerase. This sample was called 0 minutes, and further samples were taken at 2.5, 5, 7.5, 10, and 20 minutes from wild-type E. coli and the RNase III mutant. A partial biological replicate of wild-type was taken (0, 2.5, and 7.5 minutes), to examine the reproducibility between samples. PGCGROWTHCONDITIONS
Count reads aligned to each base IGVtools (version 2.3.71), window size = 1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gave a pseudocount of 0.01 to all values of 0 PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
Index and sort alignments with samtools version 1.2 PGCGROWTHCONDITIONS
Normalized decay values with average of stable genes ssrA, ssrS, and rnpB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA reduction with EpiCentre Ribo-Zero Gram Negative Ribosomal RNA reduction kit (2.5ug) & TruSeq RNA Library Prep PGCGROWTHCONDITIONS
strain: MG1693 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS
time point: time7.5 PGCGROWTHCONDITIONS
Total RNA was extracted and DNase-treated according to published protocols (Khodurksy A, Bernstein J, Peter B, Rhodius V, Wendisch V, Zimmer D. Escherichia coli Spotted Double-Strand DNA Microarrays) PGCGROWTHCONDITIONS
WTA_time7.5 PGCGROWTHCONDITIONS
Adapters trimmed with Cutadapt (v1.12) PGCGROWTHCONDITIONS
Aligned to NC_000913.3 with bwa version 0.7.7 PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
Cells were grown to exponential phase in Lysogeny broth, 37oC with shaking PGCGROWTHCONDITIONS
Cells were harvested after the addition of rifampicin  (250 μg/ml) to stop nascent transcription and quenched with stop solution (10% phenol in ethanol). The first timepoint was taken 3.5 minutes after addition of the antibiotic to give time for the diffusion of rifampicin into the cells and binding of the antibiotic to RNA polymerase. This sample was called 0 minutes, and further samples were taken at 2.5, 5, 7.5, 10, and 20 minutes from wild-type E. coli and the RNase III mutant. A partial biological replicate of wild-type was taken (0, 2.5, and 7.5 minutes), to examine the reproducibility between samples. PGCGROWTHCONDITIONS
Count reads aligned to each base IGVtools (version 2.3.71), window size = 1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gave a pseudocount of 0.01 to all values of 0 PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
Index and sort alignments with samtools version 1.2 PGCGROWTHCONDITIONS
Normalized decay values with average of stable genes ssrA, ssrS, and rnpB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA reduction with EpiCentre Ribo-Zero Gram Negative Ribosomal RNA reduction kit (2.5ug) & TruSeq RNA Library Prep PGCGROWTHCONDITIONS
strain: MG1693 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS
time point: time10 PGCGROWTHCONDITIONS
Total RNA was extracted and DNase-treated according to published protocols (Khodurksy A, Bernstein J, Peter B, Rhodius V, Wendisch V, Zimmer D. Escherichia coli Spotted Double-Strand DNA Microarrays) PGCGROWTHCONDITIONS
WTA_time10 PGCGROWTHCONDITIONS
Adapters trimmed with Cutadapt (v1.12) PGCGROWTHCONDITIONS
Aligned to NC_000913.3 with bwa version 0.7.7 PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
Cells were grown to exponential phase in Lysogeny broth, 37oC with shaking PGCGROWTHCONDITIONS
Cells were harvested after the addition of rifampicin  (250 μg/ml) to stop nascent transcription and quenched with stop solution (10% phenol in ethanol). The first timepoint was taken 3.5 minutes after addition of the antibiotic to give time for the diffusion of rifampicin into the cells and binding of the antibiotic to RNA polymerase. This sample was called 0 minutes, and further samples were taken at 2.5, 5, 7.5, 10, and 20 minutes from wild-type E. coli and the RNase III mutant. A partial biological replicate of wild-type was taken (0, 2.5, and 7.5 minutes), to examine the reproducibility between samples. PGCGROWTHCONDITIONS
Count reads aligned to each base IGVtools (version 2.3.71), window size = 1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gave a pseudocount of 0.01 to all values of 0 PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
Index and sort alignments with samtools version 1.2 PGCGROWTHCONDITIONS
Normalized decay values with average of stable genes ssrA, ssrS, and rnpB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA reduction with EpiCentre Ribo-Zero Gram Negative Ribosomal RNA reduction kit (2.5ug) & TruSeq RNA Library Prep PGCGROWTHCONDITIONS
strain: MG1693 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS
time point: time20 PGCGROWTHCONDITIONS
Total RNA was extracted and DNase-treated according to published protocols (Khodurksy A, Bernstein J, Peter B, Rhodius V, Wendisch V, Zimmer D. Escherichia coli Spotted Double-Strand DNA Microarrays) PGCGROWTHCONDITIONS
WTA_time20 PGCGROWTHCONDITIONS
Adapters trimmed with Cutadapt (v1.12) PGCGROWTHCONDITIONS
Aligned to NC_000913.3 with bwa version 0.7.7 PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
Cells were grown to exponential phase in Lysogeny broth, 37oC with shaking PGCGROWTHCONDITIONS
Cells were harvested after the addition of rifampicin  (250 μg/ml) to stop nascent transcription and quenched with stop solution (10% phenol in ethanol). The first timepoint was taken 3.5 minutes after addition of the antibiotic to give time for the diffusion of rifampicin into the cells and binding of the antibiotic to RNA polymerase. This sample was called 0 minutes, and further samples were taken at 2.5, 5, 7.5, 10, and 20 minutes from wild-type E. coli and the RNase III mutant. A partial biological replicate of wild-type was taken (0, 2.5, and 7.5 minutes), to examine the reproducibility between samples. PGCGROWTHCONDITIONS
Count reads aligned to each base IGVtools (version 2.3.71), window size = 1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gave a pseudocount of 0.01 to all values of 0 PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
Index and sort alignments with samtools version 1.2 PGCGROWTHCONDITIONS
Normalized decay values with average of stable genes ssrA, ssrS, and rnpB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA reduction with EpiCentre Ribo-Zero Gram Negative Ribosomal RNA reduction kit (2.5ug) & TruSeq RNA Library Prep PGCGROWTHCONDITIONS
strain: MG1693 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS
time point: time0 PGCGROWTHCONDITIONS
Total RNA was extracted and DNase-treated according to published protocols (Khodurksy A, Bernstein J, Peter B, Rhodius V, Wendisch V, Zimmer D. Escherichia coli Spotted Double-Strand DNA Microarrays) PGCGROWTHCONDITIONS
WTB_time0 PGCGROWTHCONDITIONS
Adapters trimmed with Cutadapt (v1.12) PGCGROWTHCONDITIONS
Aligned to NC_000913.3 with bwa version 0.7.7 PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
Cells were grown to exponential phase in Lysogeny broth, 37oC with shaking PGCGROWTHCONDITIONS
Cells were harvested after the addition of rifampicin  (250 μg/ml) to stop nascent transcription and quenched with stop solution (10% phenol in ethanol). The first timepoint was taken 3.5 minutes after addition of the antibiotic to give time for the diffusion of rifampicin into the cells and binding of the antibiotic to RNA polymerase. This sample was called 0 minutes, and further samples were taken at 2.5, 5, 7.5, 10, and 20 minutes from wild-type E. coli and the RNase III mutant. A partial biological replicate of wild-type was taken (0, 2.5, and 7.5 minutes), to examine the reproducibility between samples. PGCGROWTHCONDITIONS
Count reads aligned to each base IGVtools (version 2.3.71), window size = 1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gave a pseudocount of 0.01 to all values of 0 PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
Index and sort alignments with samtools version 1.2 PGCGROWTHCONDITIONS
Normalized decay values with average of stable genes ssrA, ssrS, and rnpB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA reduction with EpiCentre Ribo-Zero Gram Negative Ribosomal RNA reduction kit (2.5ug) & TruSeq RNA Library Prep PGCGROWTHCONDITIONS
strain: MG1693 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS
time point: time2.5 PGCGROWTHCONDITIONS
Total RNA was extracted and DNase-treated according to published protocols (Khodurksy A, Bernstein J, Peter B, Rhodius V, Wendisch V, Zimmer D. Escherichia coli Spotted Double-Strand DNA Microarrays) PGCGROWTHCONDITIONS
WTB_time2.5 PGCGROWTHCONDITIONS
Adapters trimmed with Cutadapt (v1.12) PGCGROWTHCONDITIONS
Aligned to NC_000913.3 with bwa version 0.7.7 PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
Cells were grown to exponential phase in Lysogeny broth, 37oC with shaking PGCGROWTHCONDITIONS
Cells were harvested after the addition of rifampicin  (250 μg/ml) to stop nascent transcription and quenched with stop solution (10% phenol in ethanol). The first timepoint was taken 3.5 minutes after addition of the antibiotic to give time for the diffusion of rifampicin into the cells and binding of the antibiotic to RNA polymerase. This sample was called 0 minutes, and further samples were taken at 2.5, 5, 7.5, 10, and 20 minutes from wild-type E. coli and the RNase III mutant. A partial biological replicate of wild-type was taken (0, 2.5, and 7.5 minutes), to examine the reproducibility between samples. PGCGROWTHCONDITIONS
Count reads aligned to each base IGVtools (version 2.3.71), window size = 1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gave a pseudocount of 0.01 to all values of 0 PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: wild type PGCGROWTHCONDITIONS
Index and sort alignments with samtools version 1.2 PGCGROWTHCONDITIONS
Normalized decay values with average of stable genes ssrA, ssrS, and rnpB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA reduction with EpiCentre Ribo-Zero Gram Negative Ribosomal RNA reduction kit (2.5ug) & TruSeq RNA Library Prep PGCGROWTHCONDITIONS
strain: MG1693 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS
time point: time7.5 PGCGROWTHCONDITIONS
Total RNA was extracted and DNase-treated according to published protocols (Khodurksy A, Bernstein J, Peter B, Rhodius V, Wendisch V, Zimmer D. Escherichia coli Spotted Double-Strand DNA Microarrays) PGCGROWTHCONDITIONS
WTB_time7.5 PGCGROWTHCONDITIONS
Adapters trimmed with Cutadapt (v1.12) PGCGROWTHCONDITIONS
Aligned to NC_000913.3 with bwa version 0.7.7 PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
Cells were grown to exponential phase in Lysogeny broth, 37oC with shaking PGCGROWTHCONDITIONS
Cells were harvested after the addition of rifampicin  (250 μg/ml) to stop nascent transcription and quenched with stop solution (10% phenol in ethanol). The first timepoint was taken 3.5 minutes after addition of the antibiotic to give time for the diffusion of rifampicin into the cells and binding of the antibiotic to RNA polymerase. This sample was called 0 minutes, and further samples were taken at 2.5, 5, 7.5, 10, and 20 minutes from wild-type E. coli and the RNase III mutant. A partial biological replicate of wild-type was taken (0, 2.5, and 7.5 minutes), to examine the reproducibility between samples. PGCGROWTHCONDITIONS
Count reads aligned to each base IGVtools (version 2.3.71), window size = 1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gave a pseudocount of 0.01 to all values of 0 PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: rnc- deletion mutant PGCGROWTHCONDITIONS
Index and sort alignments with samtools version 1.2 PGCGROWTHCONDITIONS
Normalized decay values with average of stable genes ssrA, ssrS, and rnpB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rnc-_time0 PGCGROWTHCONDITIONS
rRNA reduction with EpiCentre Ribo-Zero Gram Negative Ribosomal RNA reduction kit (2.5ug) & TruSeq RNA Library Prep PGCGROWTHCONDITIONS
strain: SK4455 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS
time point: time0 PGCGROWTHCONDITIONS
Total RNA was extracted and DNase-treated according to published protocols (Khodurksy A, Bernstein J, Peter B, Rhodius V, Wendisch V, Zimmer D. Escherichia coli Spotted Double-Strand DNA Microarrays) PGCGROWTHCONDITIONS
Adapters trimmed with Cutadapt (v1.12) PGCGROWTHCONDITIONS
Aligned to NC_000913.3 with bwa version 0.7.7 PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
Cells were grown to exponential phase in Lysogeny broth, 37oC with shaking PGCGROWTHCONDITIONS
Cells were harvested after the addition of rifampicin  (250 μg/ml) to stop nascent transcription and quenched with stop solution (10% phenol in ethanol). The first timepoint was taken 3.5 minutes after addition of the antibiotic to give time for the diffusion of rifampicin into the cells and binding of the antibiotic to RNA polymerase. This sample was called 0 minutes, and further samples were taken at 2.5, 5, 7.5, 10, and 20 minutes from wild-type E. coli and the RNase III mutant. A partial biological replicate of wild-type was taken (0, 2.5, and 7.5 minutes), to examine the reproducibility between samples. PGCGROWTHCONDITIONS
Count reads aligned to each base IGVtools (version 2.3.71), window size = 1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gave a pseudocount of 0.01 to all values of 0 PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: rnc- deletion mutant PGCGROWTHCONDITIONS
Index and sort alignments with samtools version 1.2 PGCGROWTHCONDITIONS
Normalized decay values with average of stable genes ssrA, ssrS, and rnpB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rnc-_time2.5 PGCGROWTHCONDITIONS
rRNA reduction with EpiCentre Ribo-Zero Gram Negative Ribosomal RNA reduction kit (2.5ug) & TruSeq RNA Library Prep PGCGROWTHCONDITIONS
strain: SK4455 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS
time point: time2.5 PGCGROWTHCONDITIONS
Total RNA was extracted and DNase-treated according to published protocols (Khodurksy A, Bernstein J, Peter B, Rhodius V, Wendisch V, Zimmer D. Escherichia coli Spotted Double-Strand DNA Microarrays) PGCGROWTHCONDITIONS
Adapters trimmed with Cutadapt (v1.12) PGCGROWTHCONDITIONS
Aligned to NC_000913.3 with bwa version 0.7.7 PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
Cells were grown to exponential phase in Lysogeny broth, 37oC with shaking PGCGROWTHCONDITIONS
Cells were harvested after the addition of rifampicin  (250 μg/ml) to stop nascent transcription and quenched with stop solution (10% phenol in ethanol). The first timepoint was taken 3.5 minutes after addition of the antibiotic to give time for the diffusion of rifampicin into the cells and binding of the antibiotic to RNA polymerase. This sample was called 0 minutes, and further samples were taken at 2.5, 5, 7.5, 10, and 20 minutes from wild-type E. coli and the RNase III mutant. A partial biological replicate of wild-type was taken (0, 2.5, and 7.5 minutes), to examine the reproducibility between samples. PGCGROWTHCONDITIONS
Count reads aligned to each base IGVtools (version 2.3.71), window size = 1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gave a pseudocount of 0.01 to all values of 0 PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: rnc- deletion mutant PGCGROWTHCONDITIONS
Index and sort alignments with samtools version 1.2 PGCGROWTHCONDITIONS
Normalized decay values with average of stable genes ssrA, ssrS, and rnpB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rnc-_time5 PGCGROWTHCONDITIONS
rRNA reduction with EpiCentre Ribo-Zero Gram Negative Ribosomal RNA reduction kit (2.5ug) & TruSeq RNA Library Prep PGCGROWTHCONDITIONS
strain: SK4455 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS
time point: time5 PGCGROWTHCONDITIONS
Total RNA was extracted and DNase-treated according to published protocols (Khodurksy A, Bernstein J, Peter B, Rhodius V, Wendisch V, Zimmer D. Escherichia coli Spotted Double-Strand DNA Microarrays) PGCGROWTHCONDITIONS
Adapters trimmed with Cutadapt (v1.12) PGCGROWTHCONDITIONS
Aligned to NC_000913.3 with bwa version 0.7.7 PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
Cells were grown to exponential phase in Lysogeny broth, 37oC with shaking PGCGROWTHCONDITIONS
Cells were harvested after the addition of rifampicin  (250 μg/ml) to stop nascent transcription and quenched with stop solution (10% phenol in ethanol). The first timepoint was taken 3.5 minutes after addition of the antibiotic to give time for the diffusion of rifampicin into the cells and binding of the antibiotic to RNA polymerase. This sample was called 0 minutes, and further samples were taken at 2.5, 5, 7.5, 10, and 20 minutes from wild-type E. coli and the RNase III mutant. A partial biological replicate of wild-type was taken (0, 2.5, and 7.5 minutes), to examine the reproducibility between samples. PGCGROWTHCONDITIONS
Count reads aligned to each base IGVtools (version 2.3.71), window size = 1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gave a pseudocount of 0.01 to all values of 0 PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: rnc- deletion mutant PGCGROWTHCONDITIONS
Index and sort alignments with samtools version 1.2 PGCGROWTHCONDITIONS
Normalized decay values with average of stable genes ssrA, ssrS, and rnpB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rnc-_time7.5 PGCGROWTHCONDITIONS
rRNA reduction with EpiCentre Ribo-Zero Gram Negative Ribosomal RNA reduction kit (2.5ug) & TruSeq RNA Library Prep PGCGROWTHCONDITIONS
strain: SK4455 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS
time point: time7.5 PGCGROWTHCONDITIONS
Total RNA was extracted and DNase-treated according to published protocols (Khodurksy A, Bernstein J, Peter B, Rhodius V, Wendisch V, Zimmer D. Escherichia coli Spotted Double-Strand DNA Microarrays) PGCGROWTHCONDITIONS
Adapters trimmed with Cutadapt (v1.12) PGCGROWTHCONDITIONS
Aligned to NC_000913.3 with bwa version 0.7.7 PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
Cells were grown to exponential phase in Lysogeny broth, 37oC with shaking PGCGROWTHCONDITIONS
Cells were harvested after the addition of rifampicin  (250 μg/ml) to stop nascent transcription and quenched with stop solution (10% phenol in ethanol). The first timepoint was taken 3.5 minutes after addition of the antibiotic to give time for the diffusion of rifampicin into the cells and binding of the antibiotic to RNA polymerase. This sample was called 0 minutes, and further samples were taken at 2.5, 5, 7.5, 10, and 20 minutes from wild-type E. coli and the RNase III mutant. A partial biological replicate of wild-type was taken (0, 2.5, and 7.5 minutes), to examine the reproducibility between samples. PGCGROWTHCONDITIONS
Count reads aligned to each base IGVtools (version 2.3.71), window size = 1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gave a pseudocount of 0.01 to all values of 0 PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: rnc- deletion mutant PGCGROWTHCONDITIONS
Index and sort alignments with samtools version 1.2 PGCGROWTHCONDITIONS
Normalized decay values with average of stable genes ssrA, ssrS, and rnpB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rnc-_time10 PGCGROWTHCONDITIONS
rRNA reduction with EpiCentre Ribo-Zero Gram Negative Ribosomal RNA reduction kit (2.5ug) & TruSeq RNA Library Prep PGCGROWTHCONDITIONS
strain: SK4455 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS
time point: time10 PGCGROWTHCONDITIONS
Total RNA was extracted and DNase-treated according to published protocols (Khodurksy A, Bernstein J, Peter B, Rhodius V, Wendisch V, Zimmer D. Escherichia coli Spotted Double-Strand DNA Microarrays) PGCGROWTHCONDITIONS
Adapters trimmed with Cutadapt (v1.12) PGCGROWTHCONDITIONS
Aligned to NC_000913.3 with bwa version 0.7.7 PGCGROWTHCONDITIONS
bacterial cells PGCGROWTHCONDITIONS
Cells were grown to exponential phase in Lysogeny broth, 37oC with shaking PGCGROWTHCONDITIONS
Cells were harvested after the addition of rifampicin  (250 μg/ml) to stop nascent transcription and quenched with stop solution (10% phenol in ethanol). The first timepoint was taken 3.5 minutes after addition of the antibiotic to give time for the diffusion of rifampicin into the cells and binding of the antibiotic to RNA polymerase. This sample was called 0 minutes, and further samples were taken at 2.5, 5, 7.5, 10, and 20 minutes from wild-type E. coli and the RNase III mutant. A partial biological replicate of wild-type was taken (0, 2.5, and 7.5 minutes), to examine the reproducibility between samples. PGCGROWTHCONDITIONS
Count reads aligned to each base IGVtools (version 2.3.71), window size = 1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Gave a pseudocount of 0.01 to all values of 0 PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
genotype/variation: rnc- deletion mutant PGCGROWTHCONDITIONS
Index and sort alignments with samtools version 1.2 PGCGROWTHCONDITIONS
Normalized decay values with average of stable genes ssrA, ssrS, and rnpB PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rnc-_time20 PGCGROWTHCONDITIONS
rRNA reduction with EpiCentre Ribo-Zero Gram Negative Ribosomal RNA reduction kit (2.5ug) & TruSeq RNA Library Prep PGCGROWTHCONDITIONS
strain: SK4455 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS
time point: time20 PGCGROWTHCONDITIONS
Total RNA was extracted and DNase-treated according to published protocols (Khodurksy A, Bernstein J, Peter B, Rhodius V, Wendisch V, Zimmer D. Escherichia coli Spotted Double-Strand DNA Microarrays) PGCGROWTHCONDITIONS
10 pmol of a pre-adenylated (rApp) adapter were ligated to 1 μg of nascent (or mature) RNA in a reaction volume of 20 μl, using 400 U T4 RNA Ligase 2, Deletion Mutant (Epicentre, cat. LR2D11310K) in the presence of 20% PEG-8000, by incubation at 25°C for 2 hours. Reaction clean-up was performed using RNA Clean & Concentrator™-5 columns, and RNA was eluted in 20 μl of Fragmentation buffer [65 mM Tris pH 8.3; 100 mM KCl; 5 mM MgCl2]. RNA was fragmented by incubation at 95°C for 8 minutes. Fragmented RNA was purified using RNA Clean & Concentrator™-5 columns, and eluted in 5.5 μl of nuclease-free water. RNA was heat-denatured at 70°C for 5 minutes, and reverse transcription was carried out in a final volume of 10 μl, in the presence of 0.5 mM dNTPs, 5 pmol of RT primer, 20 U RNaseOUT™ Recombinant Ribonuclease Inhibitor (Invitrogen, cat. 10777-019), and 100 U SuperScript® III Reverse Transcriptase (Invitrogen, cat. 18080-044), by incubation at 50°C for 50 minutes. Template RNA was degraded by adding 1 μl of 1 M NaOH, and incubating at 95°C for 5 minutes. Reaction clean-up was performed using RNA Clean & Concentrator™-5 columns, and cDNA was eluted in 6 μl nuclease-free water. cDNA fragments were resolved on a 10% TBE-Urea polyacrylamide gel, and a gel slice corresponding to fragments in the range 40-150 nt was cut. DNA was recovered by passive diffusion in Diffusion buffer for 16 hours at 37°C with moderate shaking. cDNA was precipitated by addition of 1 ml Isopropanol, and 2 μl Glycogen (20 μg/μl), and resuspended in 8.25 μl nuclease-free water. 10 pmol of a 5’-phosphorylated adapter were ligated to the 3’-OH of cDNA fragments in a final reaction volume of 25 μl, in the presence of 0.05 mM ATP, 20% PEG-4000, and 100 U CircLigase™ II ssDNA Ligase (Epicentre, cat. CL9025K), by incubation at 60°C for 4 hours, and 68°C for 2 hours. Adapter-ligated cDNA fragments were purified from excess adapter using 1.8 volumes of Agencourt AMPure XP beads (Beckman Coulter, cat. A63881), following manufacturer’s instructions. cDNA was eluted in 20 μl of nuclease-free water, and indexed sequencing adapters were introduced by 15 cycles of PCR in the presence of 25 pmol of each primer, and 25 μl NEBNext® High-Fidelity 2X PCR Master Mix (NEB, cat. M0541L). PGCGROWTHCONDITIONS
3'-end RNA-seq, Cytosolic fraction, Replicate #1 PGCGROWTHCONDITIONS
3'-end RNA-seq, Cytosolic fraction PGCGROWTHCONDITIONS
Each bacteria pellet from a 25 ml culture (OD600 ~0.3) was homogeneously resuspended in 200 µl of Buffer A [10 mM Tris pH 8.0; 20% Sucrose; 100 mM NaCl] supplemented with 200 U SUPERase• In™ RNase Inhibitor, by pipetting. 50 µl of Buffer B [50 mM EDTA; 120 mM Tris pH 8.0] supplemented with 1 µl Ready-Lyse™ Lysozyme Solution (Epicentre, cat. R1810M) were added dropwise, and the vial was gently tilted 5 times to ensure homogenous mixing. The sample was then incubated 1 minute at room temperature. 250 µl of Buffer C [0.5% Tween-20: 0.4% NaDOC; 2 M NaCl; 10 mM EDTA] were immediately added dropwise. The sample was then incubated 5 minutes at room temperature. At this stage the solution clears considerably without increasing its viscosity, and nucleoid becomes visible. Using a cut P1000 pipette tip, the whole sample was gently layered on the top of a 5-30% w/v sucrose gradient [10 mM Tris pH 8.0; 1 M NaCl; 1 mM EDTA; 1 mM DTT], and centrifuged at 17,000 RPM in a SW55Ti rotor (Beckman Coulter, cat. 342194) for 9 minutes (4°C). After centrifugation, the nucleoid fraction was collected using a syringe with a 18G blunt fill needle, and transferred to a new centrifuge tube. The remaining gradient was assumed to represent the cytosolic fraction. The nucleoid was then resuspended in 2.5 ml Wash & Resuspension buffer [40 mM Tris pH 7.5; 150 mM KCl; 10 mM MgCl2; 1 mM DTT; 0.01% Triton X-100] supplemented with 200 U SUPERase• In™ RNase Inhibitor, pulse vortexed for 5 seconds, and then centrifuged at 28,000 RPM in a SW55Ti rotor for 30 minutes (0°C). After centrifugation the supernatant was decanted, and the nucleoid pellet was washed twice with 2 ml of Wash & Resuspension buffer, taking care not to disturb it. The nucleoid was then resuspended in 500 µl Wash & Resuspension buffer, and solubilized by addition of 0.1 gr acid-washed glass beads (Sigma, cat. G1145), and shaking for 5 minutes in a TissueLyser (QIAGEN). For each 100 µl of purified nucleoids (or cytosolic fraction), 1 ml of TRIzol® Reagent (Invitrogen, cat. 15596-018) was added, and RNA was extracted following manufacturer’s instructions. RNA was analyzed on a 2100 Bioanalyzer (Agilent). In all experiments, RNA from cytosolic fraction (corresponding to mature RNA species) had RIN > 9.5. Total RNA yield from nucleoid fraction was ~6% of the total RNA content. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FastQ files were examined using the FastQC tool. Reads were clipped from 3’ adapter sequences using Cutadapt v1.10, discarding reads shorter than 15 nucleotides. Escherichia coli str. K-12 substr. MG1655 (GenBank: U00096.2) was used as the reference genome. Reads were mapped to the reference genome using Bowtie v1.1.2, by allowing up to 7 mapping positions to enable mapping to the 7 E. coli rRNA genes (parameters: -n 2 -m 7 -a --best --strata -5 5). PGCGROWTHCONDITIONS
Genome_build: U00096.2 PGCGROWTHCONDITIONS
library strategy: 3'-end RNA-seq PGCGROWTHCONDITIONS
molecule subtype: Total RNA (Cytosolic fraction) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
substr: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: DMS-seq data (pooled Total and Ribo- RNA) is provided in the form of RNA Framework's (http://www.rnaframework.com) RNA Count (RC) files. For a detailed description of the RC format, please refer to: http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Mapped reads were rescaled to a size of 10 bp, and BEDGraph files were generated using the genomeCoverageBed utility of the BEDTools suite. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: SPET-seq data is provided in the form of RNA Framework's (http://www.rnaframework.com) RNA Count (RC) files. A file corresponding to each transcription intermediate is provided. For a detailed description of the RC format, please refer to: http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: SPET-seq data (pooled Total and Ribo- RNA from both replicates) is provided in the form of RNA Framework's (http://www.rnaframework.com) RNA Count (RC) files. For each analyzed transcript, 10 files corresponding to SPET-seq data for the 10 transcription deciles are provided. For a detailed description of the RC format, please refer to: http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format PGCGROWTHCONDITIONS
10 pmol of a pre-adenylated (rApp) adapter were ligated to 1 μg of nascent (or mature) RNA in a reaction volume of 20 μl, using 400 U T4 RNA Ligase 2, Deletion Mutant (Epicentre, cat. LR2D11310K) in the presence of 20% PEG-8000, by incubation at 25°C for 2 hours. Reaction clean-up was performed using RNA Clean & Concentrator™-5 columns, and RNA was eluted in 20 μl of Fragmentation buffer [65 mM Tris pH 8.3; 100 mM KCl; 5 mM MgCl2]. RNA was fragmented by incubation at 95°C for 8 minutes. Fragmented RNA was purified using RNA Clean & Concentrator™-5 columns, and eluted in 5.5 μl of nuclease-free water. RNA was heat-denatured at 70°C for 5 minutes, and reverse transcription was carried out in a final volume of 10 μl, in the presence of 0.5 mM dNTPs, 5 pmol of RT primer, 20 U RNaseOUT™ Recombinant Ribonuclease Inhibitor (Invitrogen, cat. 10777-019), and 100 U SuperScript® III Reverse Transcriptase (Invitrogen, cat. 18080-044), by incubation at 50°C for 50 minutes. Template RNA was degraded by adding 1 μl of 1 M NaOH, and incubating at 95°C for 5 minutes. Reaction clean-up was performed using RNA Clean & Concentrator™-5 columns, and cDNA was eluted in 6 μl nuclease-free water. cDNA fragments were resolved on a 10% TBE-Urea polyacrylamide gel, and a gel slice corresponding to fragments in the range 40-150 nt was cut. DNA was recovered by passive diffusion in Diffusion buffer for 16 hours at 37°C with moderate shaking. cDNA was precipitated by addition of 1 ml Isopropanol, and 2 μl Glycogen (20 μg/μl), and resuspended in 8.25 μl nuclease-free water. 10 pmol of a 5’-phosphorylated adapter were ligated to the 3’-OH of cDNA fragments in a final reaction volume of 25 μl, in the presence of 0.05 mM ATP, 20% PEG-4000, and 100 U CircLigase™ II ssDNA Ligase (Epicentre, cat. CL9025K), by incubation at 60°C for 4 hours, and 68°C for 2 hours. Adapter-ligated cDNA fragments were purified from excess adapter using 1.8 volumes of Agencourt AMPure XP beads (Beckman Coulter, cat. A63881), following manufacturer’s instructions. cDNA was eluted in 20 μl of nuclease-free water, and indexed sequencing adapters were introduced by 15 cycles of PCR in the presence of 25 pmol of each primer, and 25 μl NEBNext® High-Fidelity 2X PCR Master Mix (NEB, cat. M0541L). PGCGROWTHCONDITIONS
3'-end RNA-seq, Cytosolic fraction, Replicate #2 PGCGROWTHCONDITIONS
3'-end RNA-seq, Cytosolic fraction PGCGROWTHCONDITIONS
Each bacteria pellet from a 25 ml culture (OD600 ~0.3) was homogeneously resuspended in 200 µl of Buffer A [10 mM Tris pH 8.0; 20% Sucrose; 100 mM NaCl] supplemented with 200 U SUPERase• In™ RNase Inhibitor, by pipetting. 50 µl of Buffer B [50 mM EDTA; 120 mM Tris pH 8.0] supplemented with 1 µl Ready-Lyse™ Lysozyme Solution (Epicentre, cat. R1810M) were added dropwise, and the vial was gently tilted 5 times to ensure homogenous mixing. The sample was then incubated 1 minute at room temperature. 250 µl of Buffer C [0.5% Tween-20: 0.4% NaDOC; 2 M NaCl; 10 mM EDTA] were immediately added dropwise. The sample was then incubated 5 minutes at room temperature. At this stage the solution clears considerably without increasing its viscosity, and nucleoid becomes visible. Using a cut P1000 pipette tip, the whole sample was gently layered on the top of a 5-30% w/v sucrose gradient [10 mM Tris pH 8.0; 1 M NaCl; 1 mM EDTA; 1 mM DTT], and centrifuged at 17,000 RPM in a SW55Ti rotor (Beckman Coulter, cat. 342194) for 9 minutes (4°C). After centrifugation, the nucleoid fraction was collected using a syringe with a 18G blunt fill needle, and transferred to a new centrifuge tube. The remaining gradient was assumed to represent the cytosolic fraction. The nucleoid was then resuspended in 2.5 ml Wash & Resuspension buffer [40 mM Tris pH 7.5; 150 mM KCl; 10 mM MgCl2; 1 mM DTT; 0.01% Triton X-100] supplemented with 200 U SUPERase• In™ RNase Inhibitor, pulse vortexed for 5 seconds, and then centrifuged at 28,000 RPM in a SW55Ti rotor for 30 minutes (0°C). After centrifugation the supernatant was decanted, and the nucleoid pellet was washed twice with 2 ml of Wash & Resuspension buffer, taking care not to disturb it. The nucleoid was then resuspended in 500 µl Wash & Resuspension buffer, and solubilized by addition of 0.1 gr acid-washed glass beads (Sigma, cat. G1145), and shaking for 5 minutes in a TissueLyser (QIAGEN). For each 100 µl of purified nucleoids (or cytosolic fraction), 1 ml of TRIzol® Reagent (Invitrogen, cat. 15596-018) was added, and RNA was extracted following manufacturer’s instructions. RNA was analyzed on a 2100 Bioanalyzer (Agilent). In all experiments, RNA from cytosolic fraction (corresponding to mature RNA species) had RIN > 9.5. Total RNA yield from nucleoid fraction was ~6% of the total RNA content. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FastQ files were examined using the FastQC tool. Reads were clipped from 3’ adapter sequences using Cutadapt v1.10, discarding reads shorter than 15 nucleotides. Escherichia coli str. K-12 substr. MG1655 (GenBank: U00096.2) was used as the reference genome. Reads were mapped to the reference genome using Bowtie v1.1.2, by allowing up to 7 mapping positions to enable mapping to the 7 E. coli rRNA genes (parameters: -n 2 -m 7 -a --best --strata -5 5). PGCGROWTHCONDITIONS
Genome_build: U00096.2 PGCGROWTHCONDITIONS
library strategy: 3'-end RNA-seq PGCGROWTHCONDITIONS
molecule subtype: Total RNA (Cytosolic fraction) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
substr: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: DMS-seq data (pooled Total and Ribo- RNA) is provided in the form of RNA Framework's (http://www.rnaframework.com) RNA Count (RC) files. For a detailed description of the RC format, please refer to: http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Mapped reads were rescaled to a size of 10 bp, and BEDGraph files were generated using the genomeCoverageBed utility of the BEDTools suite. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: SPET-seq data is provided in the form of RNA Framework's (http://www.rnaframework.com) RNA Count (RC) files. A file corresponding to each transcription intermediate is provided. For a detailed description of the RC format, please refer to: http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: SPET-seq data (pooled Total and Ribo- RNA from both replicates) is provided in the form of RNA Framework's (http://www.rnaframework.com) RNA Count (RC) files. For each analyzed transcript, 10 files corresponding to SPET-seq data for the 10 transcription deciles are provided. For a detailed description of the RC format, please refer to: http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format PGCGROWTHCONDITIONS
10 pmol of a pre-adenylated (rApp) adapter were ligated to 1 μg of nascent (or mature) RNA in a reaction volume of 20 μl, using 400 U T4 RNA Ligase 2, Deletion Mutant (Epicentre, cat. LR2D11310K) in the presence of 20% PEG-8000, by incubation at 25°C for 2 hours. Reaction clean-up was performed using RNA Clean & Concentrator™-5 columns, and RNA was eluted in 20 μl of Fragmentation buffer [65 mM Tris pH 8.3; 100 mM KCl; 5 mM MgCl2]. RNA was fragmented by incubation at 95°C for 8 minutes. Fragmented RNA was purified using RNA Clean & Concentrator™-5 columns, and eluted in 5.5 μl of nuclease-free water. RNA was heat-denatured at 70°C for 5 minutes, and reverse transcription was carried out in a final volume of 10 μl, in the presence of 0.5 mM dNTPs, 5 pmol of RT primer, 20 U RNaseOUT™ Recombinant Ribonuclease Inhibitor (Invitrogen, cat. 10777-019), and 100 U SuperScript® III Reverse Transcriptase (Invitrogen, cat. 18080-044), by incubation at 50°C for 50 minutes. Template RNA was degraded by adding 1 μl of 1 M NaOH, and incubating at 95°C for 5 minutes. Reaction clean-up was performed using RNA Clean & Concentrator™-5 columns, and cDNA was eluted in 6 μl nuclease-free water. cDNA fragments were resolved on a 10% TBE-Urea polyacrylamide gel, and a gel slice corresponding to fragments in the range 40-150 nt was cut. DNA was recovered by passive diffusion in Diffusion buffer for 16 hours at 37°C with moderate shaking. cDNA was precipitated by addition of 1 ml Isopropanol, and 2 μl Glycogen (20 μg/μl), and resuspended in 8.25 μl nuclease-free water. 10 pmol of a 5’-phosphorylated adapter were ligated to the 3’-OH of cDNA fragments in a final reaction volume of 25 μl, in the presence of 0.05 mM ATP, 20% PEG-4000, and 100 U CircLigase™ II ssDNA Ligase (Epicentre, cat. CL9025K), by incubation at 60°C for 4 hours, and 68°C for 2 hours. Adapter-ligated cDNA fragments were purified from excess adapter using 1.8 volumes of Agencourt AMPure XP beads (Beckman Coulter, cat. A63881), following manufacturer’s instructions. cDNA was eluted in 20 μl of nuclease-free water, and indexed sequencing adapters were introduced by 15 cycles of PCR in the presence of 25 pmol of each primer, and 25 μl NEBNext® High-Fidelity 2X PCR Master Mix (NEB, cat. M0541L). PGCGROWTHCONDITIONS
3'-end RNA-seq, Nucleoid fraction, Replicate #1 PGCGROWTHCONDITIONS
3'-end RNA-seq, Nucleoid fraction PGCGROWTHCONDITIONS
Each bacteria pellet from a 25 ml culture (OD600 ~0.3) was homogeneously resuspended in 200 µl of Buffer A [10 mM Tris pH 8.0; 20% Sucrose; 100 mM NaCl] supplemented with 200 U SUPERase• In™ RNase Inhibitor, by pipetting. 50 µl of Buffer B [50 mM EDTA; 120 mM Tris pH 8.0] supplemented with 1 µl Ready-Lyse™ Lysozyme Solution (Epicentre, cat. R1810M) were added dropwise, and the vial was gently tilted 5 times to ensure homogenous mixing. The sample was then incubated 1 minute at room temperature. 250 µl of Buffer C [0.5% Tween-20: 0.4% NaDOC; 2 M NaCl; 10 mM EDTA] were immediately added dropwise. The sample was then incubated 5 minutes at room temperature. At this stage the solution clears considerably without increasing its viscosity, and nucleoid becomes visible. Using a cut P1000 pipette tip, the whole sample was gently layered on the top of a 5-30% w/v sucrose gradient [10 mM Tris pH 8.0; 1 M NaCl; 1 mM EDTA; 1 mM DTT], and centrifuged at 17,000 RPM in a SW55Ti rotor (Beckman Coulter, cat. 342194) for 9 minutes (4°C). After centrifugation, the nucleoid fraction was collected using a syringe with a 18G blunt fill needle, and transferred to a new centrifuge tube. The remaining gradient was assumed to represent the cytosolic fraction. The nucleoid was then resuspended in 2.5 ml Wash & Resuspension buffer [40 mM Tris pH 7.5; 150 mM KCl; 10 mM MgCl2; 1 mM DTT; 0.01% Triton X-100] supplemented with 200 U SUPERase• In™ RNase Inhibitor, pulse vortexed for 5 seconds, and then centrifuged at 28,000 RPM in a SW55Ti rotor for 30 minutes (0°C). After centrifugation the supernatant was decanted, and the nucleoid pellet was washed twice with 2 ml of Wash & Resuspension buffer, taking care not to disturb it. The nucleoid was then resuspended in 500 µl Wash & Resuspension buffer, and solubilized by addition of 0.1 gr acid-washed glass beads (Sigma, cat. G1145), and shaking for 5 minutes in a TissueLyser (QIAGEN). For each 100 µl of purified nucleoids (or cytosolic fraction), 1 ml of TRIzol® Reagent (Invitrogen, cat. 15596-018) was added, and RNA was extracted following manufacturer’s instructions. RNA was analyzed on a 2100 Bioanalyzer (Agilent). In all experiments, RNA from cytosolic fraction (corresponding to mature RNA species) had RIN > 9.5. Total RNA yield from nucleoid fraction was ~6% of the total RNA content. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FastQ files were examined using the FastQC tool. Reads were clipped from 3’ adapter sequences using Cutadapt v1.10, discarding reads shorter than 15 nucleotides. Escherichia coli str. K-12 substr. MG1655 (GenBank: U00096.2) was used as the reference genome. Reads were mapped to the reference genome using Bowtie v1.1.2, by allowing up to 7 mapping positions to enable mapping to the 7 E. coli rRNA genes (parameters: -n 2 -m 7 -a --best --strata -5 5). PGCGROWTHCONDITIONS
Genome_build: U00096.2 PGCGROWTHCONDITIONS
library strategy: 3'-end RNA-seq PGCGROWTHCONDITIONS
molecule subtype: Total RNA (Nucleoid fraction) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
substr: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: DMS-seq data (pooled Total and Ribo- RNA) is provided in the form of RNA Framework's (http://www.rnaframework.com) RNA Count (RC) files. For a detailed description of the RC format, please refer to: http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Mapped reads were rescaled to a size of 10 bp, and BEDGraph files were generated using the genomeCoverageBed utility of the BEDTools suite. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: SPET-seq data is provided in the form of RNA Framework's (http://www.rnaframework.com) RNA Count (RC) files. A file corresponding to each transcription intermediate is provided. For a detailed description of the RC format, please refer to: http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: SPET-seq data (pooled Total and Ribo- RNA from both replicates) is provided in the form of RNA Framework's (http://www.rnaframework.com) RNA Count (RC) files. For each analyzed transcript, 10 files corresponding to SPET-seq data for the 10 transcription deciles are provided. For a detailed description of the RC format, please refer to: http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format PGCGROWTHCONDITIONS
10 pmol of a pre-adenylated (rApp) adapter were ligated to 1 μg of nascent (or mature) RNA in a reaction volume of 20 μl, using 400 U T4 RNA Ligase 2, Deletion Mutant (Epicentre, cat. LR2D11310K) in the presence of 20% PEG-8000, by incubation at 25°C for 2 hours. Reaction clean-up was performed using RNA Clean & Concentrator™-5 columns, and RNA was eluted in 20 μl of Fragmentation buffer [65 mM Tris pH 8.3; 100 mM KCl; 5 mM MgCl2]. RNA was fragmented by incubation at 95°C for 8 minutes. Fragmented RNA was purified using RNA Clean & Concentrator™-5 columns, and eluted in 5.5 μl of nuclease-free water. RNA was heat-denatured at 70°C for 5 minutes, and reverse transcription was carried out in a final volume of 10 μl, in the presence of 0.5 mM dNTPs, 5 pmol of RT primer, 20 U RNaseOUT™ Recombinant Ribonuclease Inhibitor (Invitrogen, cat. 10777-019), and 100 U SuperScript® III Reverse Transcriptase (Invitrogen, cat. 18080-044), by incubation at 50°C for 50 minutes. Template RNA was degraded by adding 1 μl of 1 M NaOH, and incubating at 95°C for 5 minutes. Reaction clean-up was performed using RNA Clean & Concentrator™-5 columns, and cDNA was eluted in 6 μl nuclease-free water. cDNA fragments were resolved on a 10% TBE-Urea polyacrylamide gel, and a gel slice corresponding to fragments in the range 40-150 nt was cut. DNA was recovered by passive diffusion in Diffusion buffer for 16 hours at 37°C with moderate shaking. cDNA was precipitated by addition of 1 ml Isopropanol, and 2 μl Glycogen (20 μg/μl), and resuspended in 8.25 μl nuclease-free water. 10 pmol of a 5’-phosphorylated adapter were ligated to the 3’-OH of cDNA fragments in a final reaction volume of 25 μl, in the presence of 0.05 mM ATP, 20% PEG-4000, and 100 U CircLigase™ II ssDNA Ligase (Epicentre, cat. CL9025K), by incubation at 60°C for 4 hours, and 68°C for 2 hours. Adapter-ligated cDNA fragments were purified from excess adapter using 1.8 volumes of Agencourt AMPure XP beads (Beckman Coulter, cat. A63881), following manufacturer’s instructions. cDNA was eluted in 20 μl of nuclease-free water, and indexed sequencing adapters were introduced by 15 cycles of PCR in the presence of 25 pmol of each primer, and 25 μl NEBNext® High-Fidelity 2X PCR Master Mix (NEB, cat. M0541L). PGCGROWTHCONDITIONS
3'-end RNA-seq, Nucleoid fraction, Replicate #2 PGCGROWTHCONDITIONS
3'-end RNA-seq, Nucleoid fraction PGCGROWTHCONDITIONS
Each bacteria pellet from a 25 ml culture (OD600 ~0.3) was homogeneously resuspended in 200 µl of Buffer A [10 mM Tris pH 8.0; 20% Sucrose; 100 mM NaCl] supplemented with 200 U SUPERase• In™ RNase Inhibitor, by pipetting. 50 µl of Buffer B [50 mM EDTA; 120 mM Tris pH 8.0] supplemented with 1 µl Ready-Lyse™ Lysozyme Solution (Epicentre, cat. R1810M) were added dropwise, and the vial was gently tilted 5 times to ensure homogenous mixing. The sample was then incubated 1 minute at room temperature. 250 µl of Buffer C [0.5% Tween-20: 0.4% NaDOC; 2 M NaCl; 10 mM EDTA] were immediately added dropwise. The sample was then incubated 5 minutes at room temperature. At this stage the solution clears considerably without increasing its viscosity, and nucleoid becomes visible. Using a cut P1000 pipette tip, the whole sample was gently layered on the top of a 5-30% w/v sucrose gradient [10 mM Tris pH 8.0; 1 M NaCl; 1 mM EDTA; 1 mM DTT], and centrifuged at 17,000 RPM in a SW55Ti rotor (Beckman Coulter, cat. 342194) for 9 minutes (4°C). After centrifugation, the nucleoid fraction was collected using a syringe with a 18G blunt fill needle, and transferred to a new centrifuge tube. The remaining gradient was assumed to represent the cytosolic fraction. The nucleoid was then resuspended in 2.5 ml Wash & Resuspension buffer [40 mM Tris pH 7.5; 150 mM KCl; 10 mM MgCl2; 1 mM DTT; 0.01% Triton X-100] supplemented with 200 U SUPERase• In™ RNase Inhibitor, pulse vortexed for 5 seconds, and then centrifuged at 28,000 RPM in a SW55Ti rotor for 30 minutes (0°C). After centrifugation the supernatant was decanted, and the nucleoid pellet was washed twice with 2 ml of Wash & Resuspension buffer, taking care not to disturb it. The nucleoid was then resuspended in 500 µl Wash & Resuspension buffer, and solubilized by addition of 0.1 gr acid-washed glass beads (Sigma, cat. G1145), and shaking for 5 minutes in a TissueLyser (QIAGEN). For each 100 µl of purified nucleoids (or cytosolic fraction), 1 ml of TRIzol® Reagent (Invitrogen, cat. 15596-018) was added, and RNA was extracted following manufacturer’s instructions. RNA was analyzed on a 2100 Bioanalyzer (Agilent). In all experiments, RNA from cytosolic fraction (corresponding to mature RNA species) had RIN > 9.5. Total RNA yield from nucleoid fraction was ~6% of the total RNA content. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
FastQ files were examined using the FastQC tool. Reads were clipped from 3’ adapter sequences using Cutadapt v1.10, discarding reads shorter than 15 nucleotides. Escherichia coli str. K-12 substr. MG1655 (GenBank: U00096.2) was used as the reference genome. Reads were mapped to the reference genome using Bowtie v1.1.2, by allowing up to 7 mapping positions to enable mapping to the 7 E. coli rRNA genes (parameters: -n 2 -m 7 -a --best --strata -5 5). PGCGROWTHCONDITIONS
Genome_build: U00096.2 PGCGROWTHCONDITIONS
library strategy: 3'-end RNA-seq PGCGROWTHCONDITIONS
molecule subtype: Total RNA (Nucleoid fraction) PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
substr: MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: DMS-seq data (pooled Total and Ribo- RNA) is provided in the form of RNA Framework's (http://www.rnaframework.com) RNA Count (RC) files. For a detailed description of the RC format, please refer to: http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Mapped reads were rescaled to a size of 10 bp, and BEDGraph files were generated using the genomeCoverageBed utility of the BEDTools suite. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: SPET-seq data is provided in the form of RNA Framework's (http://www.rnaframework.com) RNA Count (RC) files. A file corresponding to each transcription intermediate is provided. For a detailed description of the RC format, please refer to: http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: SPET-seq data (pooled Total and Ribo- RNA from both replicates) is provided in the form of RNA Framework's (http://www.rnaframework.com) RNA Count (RC) files. For each analyzed transcript, 10 files corresponding to SPET-seq data for the 10 transcription deciles are provided. For a detailed description of the RC format, please refer to: http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format PGCGROWTHCONDITIONS
1A_MG_t0 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 - unexposed at t0 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
2A_MG_t10 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 - unexposed at t10 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
3A_MG_t30 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 - unexposed at t30 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
4A_MG_t60 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 - unexposed at t60 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
5A_MG+Hg_t10 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM HgCl2 at t10 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
6A_MG+Hg_t30 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM HgCl2 at t30 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
7A_MG+Hg_t60 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM HgCl2 at t60 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
8A_MG+PMA_t10 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM PMA at t10 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
9A_MG+PMA_t30 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM PMA at t30 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
10A_MG+PMA_t60 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM PMA at t60 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
1B_MG_t0 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 - unexposed at t0 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
2B_MG_t10 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 - unexposed at t10 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
3B_MG_t30 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 - unexposed at t30 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
4B_MG_t60 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 - unexposed at t60 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
5B_MG+Hg_t10 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM HgCl2 at t10 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
6B_MG+Hg_t30 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM HgCl2 at t30 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
7B_MG+Hg_t60 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM HgCl2 at t60 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
8B_MG+PMA_t10 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM PMA at t10 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
9B_MG+PMA_t30 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM PMA at t30 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
10B_MG+PMA_t60 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM PMA at t60 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
1C_MG_t0 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 - unexposed at t0 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
2C_MG_t10 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 - unexposed at t10 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
3C_MG_t30 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 - unexposed at t30 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
4C_MG_t60 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 - unexposed at t60 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
5C_MG+Hg_t10 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM HgCl2 at t10 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
6C_MG+Hg_t30 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM HgCl2 at t30 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
7C_MG+Hg_t60 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM HgCl2 at t60 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
8C_MG+PMA_t10 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM PMA at t10 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
9C_MG+PMA_t30 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM PMA at t30 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
10C_MG+PMA_t60 PGCGROWTHCONDITIONS
E. coli PGCGROWTHCONDITIONS
Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format. PGCGROWTHCONDITIONS
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf ) PGCGROWTHCONDITIONS
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control. PGCGROWTHCONDITIONS
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions. PGCGROWTHCONDITIONS
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format PGCGROWTHCONDITIONS
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode. PGCGROWTHCONDITIONS
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations. PGCGROWTHCONDITIONS
treatment: MG1655 + 3µM PMA at t60 PGCGROWTHCONDITIONS
When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection. PGCGROWTHCONDITIONS
Bacteria cells PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP009273.1 PGCGROWTHCONDITIONS
product: Butanol PGCGROWTHCONDITIONS
Quantification of gene expression and analysis of gene differential expression were performed using Fragment Per Kilo bases per Million reads (FPKM) value based rsem software version 1.2.4 and edgeR version 3.4.2 (Bioconductor), respectively PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CP009273.1 whole genome using bowtie2 PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel file include FPKM values of different genes for each sample PGCGROWTHCONDITIONS
Total RNAs were isolated using TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries. PGCGROWTHCONDITIONS
WT_6h_rep1 PGCGROWTHCONDITIONS
Bacteria cells PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP009273.1 PGCGROWTHCONDITIONS
product: Butanol PGCGROWTHCONDITIONS
Quantification of gene expression and analysis of gene differential expression were performed using Fragment Per Kilo bases per Million reads (FPKM) value based rsem software version 1.2.4 and edgeR version 3.4.2 (Bioconductor), respectively PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CP009273.1 whole genome using bowtie2 PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel file include FPKM values of different genes for each sample PGCGROWTHCONDITIONS
Total RNAs were isolated using TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries. PGCGROWTHCONDITIONS
WT_6h_rep2 PGCGROWTHCONDITIONS
Bacteria cells PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP009273.1 PGCGROWTHCONDITIONS
product: Butanol PGCGROWTHCONDITIONS
Quantification of gene expression and analysis of gene differential expression were performed using Fragment Per Kilo bases per Million reads (FPKM) value based rsem software version 1.2.4 and edgeR version 3.4.2 (Bioconductor), respectively PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CP009273.1 whole genome using bowtie2 PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel file include FPKM values of different genes for each sample PGCGROWTHCONDITIONS
Total RNAs were isolated using TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries. PGCGROWTHCONDITIONS
WT_12h_rep1 PGCGROWTHCONDITIONS
Bacteria cells PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP009273.1 PGCGROWTHCONDITIONS
product: Butanol PGCGROWTHCONDITIONS
Quantification of gene expression and analysis of gene differential expression were performed using Fragment Per Kilo bases per Million reads (FPKM) value based rsem software version 1.2.4 and edgeR version 3.4.2 (Bioconductor), respectively PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CP009273.1 whole genome using bowtie2 PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel file include FPKM values of different genes for each sample PGCGROWTHCONDITIONS
Total RNAs were isolated using TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries. PGCGROWTHCONDITIONS
WT_12h_rep2 PGCGROWTHCONDITIONS
Bacteria cells PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP009273.1 PGCGROWTHCONDITIONS
product: Butanol PGCGROWTHCONDITIONS
Quantification of gene expression and analysis of gene differential expression were performed using Fragment Per Kilo bases per Million reads (FPKM) value based rsem software version 1.2.4 and edgeR version 3.4.2 (Bioconductor), respectively PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CP009273.1 whole genome using bowtie2 PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel file include FPKM values of different genes for each sample PGCGROWTHCONDITIONS
Total RNAs were isolated using TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries. PGCGROWTHCONDITIONS
WT_24h_rep1 PGCGROWTHCONDITIONS
Bacteria cells PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP009273.1 PGCGROWTHCONDITIONS
product: Butanol PGCGROWTHCONDITIONS
Quantification of gene expression and analysis of gene differential expression were performed using Fragment Per Kilo bases per Million reads (FPKM) value based rsem software version 1.2.4 and edgeR version 3.4.2 (Bioconductor), respectively PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CP009273.1 whole genome using bowtie2 PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel file include FPKM values of different genes for each sample PGCGROWTHCONDITIONS
Total RNAs were isolated using TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries. PGCGROWTHCONDITIONS
WT_24h_rep2 PGCGROWTHCONDITIONS
Bacteria cells PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP009273.1 PGCGROWTHCONDITIONS
product: Butanol PGCGROWTHCONDITIONS
Quantification of gene expression and analysis of gene differential expression were performed using Fragment Per Kilo bases per Million reads (FPKM) value based rsem software version 1.2.4 and edgeR version 3.4.2 (Bioconductor), respectively PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CP009273.1 whole genome using bowtie2 PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel file include FPKM values of different genes for each sample PGCGROWTHCONDITIONS
Total RNAs were isolated using TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries. PGCGROWTHCONDITIONS
WT_48h_rep1 PGCGROWTHCONDITIONS
Bacteria cells PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP009273.1 PGCGROWTHCONDITIONS
product: Butanol PGCGROWTHCONDITIONS
Quantification of gene expression and analysis of gene differential expression were performed using Fragment Per Kilo bases per Million reads (FPKM) value based rsem software version 1.2.4 and edgeR version 3.4.2 (Bioconductor), respectively PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CP009273.1 whole genome using bowtie2 PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel file include FPKM values of different genes for each sample PGCGROWTHCONDITIONS
Total RNAs were isolated using TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries. PGCGROWTHCONDITIONS
WT_48h_rep2 PGCGROWTHCONDITIONS
Bacteria cells PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP009273.1 PGCGROWTHCONDITIONS
MT_6h_rep1 PGCGROWTHCONDITIONS
product: Butanol PGCGROWTHCONDITIONS
Quantification of gene expression and analysis of gene differential expression were performed using Fragment Per Kilo bases per Million reads (FPKM) value based rsem software version 1.2.4 and edgeR version 3.4.2 (Bioconductor), respectively PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CP009273.1 whole genome using bowtie2 PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel file include FPKM values of different genes for each sample PGCGROWTHCONDITIONS
Total RNAs were isolated using TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries. PGCGROWTHCONDITIONS
Bacteria cells PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP009273.1 PGCGROWTHCONDITIONS
MT_6h_rep2 PGCGROWTHCONDITIONS
product: Butanol PGCGROWTHCONDITIONS
Quantification of gene expression and analysis of gene differential expression were performed using Fragment Per Kilo bases per Million reads (FPKM) value based rsem software version 1.2.4 and edgeR version 3.4.2 (Bioconductor), respectively PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CP009273.1 whole genome using bowtie2 PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel file include FPKM values of different genes for each sample PGCGROWTHCONDITIONS
Total RNAs were isolated using TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries. PGCGROWTHCONDITIONS
Bacteria cells PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP009273.1 PGCGROWTHCONDITIONS
MT_12h_rep1 PGCGROWTHCONDITIONS
product: Butanol PGCGROWTHCONDITIONS
Quantification of gene expression and analysis of gene differential expression were performed using Fragment Per Kilo bases per Million reads (FPKM) value based rsem software version 1.2.4 and edgeR version 3.4.2 (Bioconductor), respectively PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CP009273.1 whole genome using bowtie2 PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel file include FPKM values of different genes for each sample PGCGROWTHCONDITIONS
Total RNAs were isolated using TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries. PGCGROWTHCONDITIONS
Bacteria cells PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP009273.1 PGCGROWTHCONDITIONS
MT_12h_rep2 PGCGROWTHCONDITIONS
product: Butanol PGCGROWTHCONDITIONS
Quantification of gene expression and analysis of gene differential expression were performed using Fragment Per Kilo bases per Million reads (FPKM) value based rsem software version 1.2.4 and edgeR version 3.4.2 (Bioconductor), respectively PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CP009273.1 whole genome using bowtie2 PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel file include FPKM values of different genes for each sample PGCGROWTHCONDITIONS
Total RNAs were isolated using TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries. PGCGROWTHCONDITIONS
Bacteria cells PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP009273.1 PGCGROWTHCONDITIONS
MT_24h_rep1 PGCGROWTHCONDITIONS
product: Butanol PGCGROWTHCONDITIONS
Quantification of gene expression and analysis of gene differential expression were performed using Fragment Per Kilo bases per Million reads (FPKM) value based rsem software version 1.2.4 and edgeR version 3.4.2 (Bioconductor), respectively PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CP009273.1 whole genome using bowtie2 PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel file include FPKM values of different genes for each sample PGCGROWTHCONDITIONS
Total RNAs were isolated using TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries. PGCGROWTHCONDITIONS
Bacteria cells PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP009273.1 PGCGROWTHCONDITIONS
MT_24h_rep2 PGCGROWTHCONDITIONS
product: Butanol PGCGROWTHCONDITIONS
Quantification of gene expression and analysis of gene differential expression were performed using Fragment Per Kilo bases per Million reads (FPKM) value based rsem software version 1.2.4 and edgeR version 3.4.2 (Bioconductor), respectively PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CP009273.1 whole genome using bowtie2 PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel file include FPKM values of different genes for each sample PGCGROWTHCONDITIONS
Total RNAs were isolated using TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries. PGCGROWTHCONDITIONS
Bacteria cells PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP009273.1 PGCGROWTHCONDITIONS
MT_48h_rep1 PGCGROWTHCONDITIONS
product: Butanol PGCGROWTHCONDITIONS
Quantification of gene expression and analysis of gene differential expression were performed using Fragment Per Kilo bases per Million reads (FPKM) value based rsem software version 1.2.4 and edgeR version 3.4.2 (Bioconductor), respectively PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CP009273.1 whole genome using bowtie2 PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel file include FPKM values of different genes for each sample PGCGROWTHCONDITIONS
Total RNAs were isolated using TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries. PGCGROWTHCONDITIONS
Bacteria cells PGCGROWTHCONDITIONS
Basecalls performed using CASAVA version 1.8.2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: CP009273.1 PGCGROWTHCONDITIONS
MT_48h_rep2 PGCGROWTHCONDITIONS
product: Butanol PGCGROWTHCONDITIONS
Quantification of gene expression and analysis of gene differential expression were performed using Fragment Per Kilo bases per Million reads (FPKM) value based rsem software version 1.2.4 and edgeR version 3.4.2 (Bioconductor), respectively PGCGROWTHCONDITIONS
RNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CP009273.1 whole genome using bowtie2 PGCGROWTHCONDITIONS
strain: BW25113 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Excel file include FPKM values of different genes for each sample PGCGROWTHCONDITIONS
Total RNAs were isolated using TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries. PGCGROWTHCONDITIONS
cell culture PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Fragmentation and reverse transcription of RNA with random primers was carried out using the NEB First Strand Synthesis Module (New England Biolabs). Second strand synthesis was done with the NEBNext Ultra Directional RNA Second Strand Synthesis Module (New England Biolabs), then purified with 1.7x AMPURE Bead XP (Beckman Coulter). DNA end repair was carried out with the NEBNext end repair module, dA-tailing used the NEBNext dA-Tailing Module and adapter ligation used the NEBNext Quick Ligation module (New England Biolabs). PCR amplification was carried out for 10 rounds of synthesis using the NEBNext High-Fidelity PCR Master Mix with NEBNext USER Enzyme (New England Biolabs), samples were purified with 1.0x AMPURE Bead XP (Beckman Coulter). Library quality was verified on a Bio-Analyzer DNA chip (Agilent). PGCGROWTHCONDITIONS
Genome_build: U00096.3 (E. coli K12) and NC_001604.1 (T7), excluding ribosomal genes, and with recoded gene 10 sequence (Bull, 2012, PMCID: PMC3457771) in place of wild-type sequence for analysis of recoded and evolved strains PGCGROWTHCONDITIONS
infection: T7 PGCGROWTHCONDITIONS
pseudoalignment and quantitation with kallisto v0.42.5 with parameters --single -l 450 -s 250 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using Trizol reagent (Thermo Fisher Scientific) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimitted text files contain TPM (transcripts per million) values for each sample PGCGROWTHCONDITIONS
t7 genotype: wild-type gene 10 PGCGROWTHCONDITIONS
t7 strain: wild type PGCGROWTHCONDITIONS
time: 1 min post-infection PGCGROWTHCONDITIONS
WT 1min rep7 PGCGROWTHCONDITIONS
cell culture PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Fragmentation and reverse transcription of RNA with random primers was carried out using the NEB First Strand Synthesis Module (New England Biolabs). Second strand synthesis was done with the NEBNext Ultra Directional RNA Second Strand Synthesis Module (New England Biolabs), then purified with 1.7x AMPURE Bead XP (Beckman Coulter). DNA end repair was carried out with the NEBNext end repair module, dA-tailing used the NEBNext dA-Tailing Module and adapter ligation used the NEBNext Quick Ligation module (New England Biolabs). PCR amplification was carried out for 10 rounds of synthesis using the NEBNext High-Fidelity PCR Master Mix with NEBNext USER Enzyme (New England Biolabs), samples were purified with 1.0x AMPURE Bead XP (Beckman Coulter). Library quality was verified on a Bio-Analyzer DNA chip (Agilent). PGCGROWTHCONDITIONS
Genome_build: U00096.3 (E. coli K12) and NC_001604.1 (T7), excluding ribosomal genes, and with recoded gene 10 sequence (Bull, 2012, PMCID: PMC3457771) in place of wild-type sequence for analysis of recoded and evolved strains PGCGROWTHCONDITIONS
infection: T7 PGCGROWTHCONDITIONS
pseudoalignment and quantitation with kallisto v0.42.5 with parameters --single -l 450 -s 250 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using Trizol reagent (Thermo Fisher Scientific) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimitted text files contain TPM (transcripts per million) values for each sample PGCGROWTHCONDITIONS
t7 genotype: wild-type gene 10 PGCGROWTHCONDITIONS
t7 strain: wild type PGCGROWTHCONDITIONS
time: 9 min post-infection PGCGROWTHCONDITIONS
WT 9min rep7 PGCGROWTHCONDITIONS
cell culture PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Fragmentation and reverse transcription of RNA with random primers was carried out using the NEB First Strand Synthesis Module (New England Biolabs). Second strand synthesis was done with the NEBNext Ultra Directional RNA Second Strand Synthesis Module (New England Biolabs), then purified with 1.7x AMPURE Bead XP (Beckman Coulter). DNA end repair was carried out with the NEBNext end repair module, dA-tailing used the NEBNext dA-Tailing Module and adapter ligation used the NEBNext Quick Ligation module (New England Biolabs). PCR amplification was carried out for 10 rounds of synthesis using the NEBNext High-Fidelity PCR Master Mix with NEBNext USER Enzyme (New England Biolabs), samples were purified with 1.0x AMPURE Bead XP (Beckman Coulter). Library quality was verified on a Bio-Analyzer DNA chip (Agilent). PGCGROWTHCONDITIONS
Genome_build: U00096.3 (E. coli K12) and NC_001604.1 (T7), excluding ribosomal genes, and with recoded gene 10 sequence (Bull, 2012, PMCID: PMC3457771) in place of wild-type sequence for analysis of recoded and evolved strains PGCGROWTHCONDITIONS
infection: T7 PGCGROWTHCONDITIONS
pseudoalignment and quantitation with kallisto v0.42.5 with parameters --single -l 450 -s 250 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using Trizol reagent (Thermo Fisher Scientific) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimitted text files contain TPM (transcripts per million) values for each sample PGCGROWTHCONDITIONS
t7 genotype: wild-type gene 10 PGCGROWTHCONDITIONS
t7 strain: wild type PGCGROWTHCONDITIONS
time: 9 min post-infection PGCGROWTHCONDITIONS
WT 9min rep8 PGCGROWTHCONDITIONS
cell culture PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
evolved 1min rep6 PGCGROWTHCONDITIONS
Fragmentation and reverse transcription of RNA with random primers was carried out using the NEB First Strand Synthesis Module (New England Biolabs). Second strand synthesis was done with the NEBNext Ultra Directional RNA Second Strand Synthesis Module (New England Biolabs), then purified with 1.7x AMPURE Bead XP (Beckman Coulter). DNA end repair was carried out with the NEBNext end repair module, dA-tailing used the NEBNext dA-Tailing Module and adapter ligation used the NEBNext Quick Ligation module (New England Biolabs). PCR amplification was carried out for 10 rounds of synthesis using the NEBNext High-Fidelity PCR Master Mix with NEBNext USER Enzyme (New England Biolabs), samples were purified with 1.0x AMPURE Bead XP (Beckman Coulter). Library quality was verified on a Bio-Analyzer DNA chip (Agilent). PGCGROWTHCONDITIONS
Genome_build: U00096.3 (E. coli K12) and NC_001604.1 (T7), excluding ribosomal genes, and with recoded gene 10 sequence (Bull, 2012, PMCID: PMC3457771) in place of wild-type sequence for analysis of recoded and evolved strains PGCGROWTHCONDITIONS
infection: T7 PGCGROWTHCONDITIONS
pseudoalignment and quantitation with kallisto v0.42.5 with parameters --single -l 450 -s 250 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using Trizol reagent (Thermo Fisher Scientific) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimitted text files contain TPM (transcripts per million) values for each sample PGCGROWTHCONDITIONS
t7 genotype: evolved, codon-deoptimized gene 10 PGCGROWTHCONDITIONS
t7 strain: evolved PGCGROWTHCONDITIONS
time: 1 min post-infection PGCGROWTHCONDITIONS
cell culture PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
evolved 1min rep8 PGCGROWTHCONDITIONS
Fragmentation and reverse transcription of RNA with random primers was carried out using the NEB First Strand Synthesis Module (New England Biolabs). Second strand synthesis was done with the NEBNext Ultra Directional RNA Second Strand Synthesis Module (New England Biolabs), then purified with 1.7x AMPURE Bead XP (Beckman Coulter). DNA end repair was carried out with the NEBNext end repair module, dA-tailing used the NEBNext dA-Tailing Module and adapter ligation used the NEBNext Quick Ligation module (New England Biolabs). PCR amplification was carried out for 10 rounds of synthesis using the NEBNext High-Fidelity PCR Master Mix with NEBNext USER Enzyme (New England Biolabs), samples were purified with 1.0x AMPURE Bead XP (Beckman Coulter). Library quality was verified on a Bio-Analyzer DNA chip (Agilent). PGCGROWTHCONDITIONS
Genome_build: U00096.3 (E. coli K12) and NC_001604.1 (T7), excluding ribosomal genes, and with recoded gene 10 sequence (Bull, 2012, PMCID: PMC3457771) in place of wild-type sequence for analysis of recoded and evolved strains PGCGROWTHCONDITIONS
infection: T7 PGCGROWTHCONDITIONS
pseudoalignment and quantitation with kallisto v0.42.5 with parameters --single -l 450 -s 250 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using Trizol reagent (Thermo Fisher Scientific) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimitted text files contain TPM (transcripts per million) values for each sample PGCGROWTHCONDITIONS
t7 genotype: evolved, codon-deoptimized gene 10 PGCGROWTHCONDITIONS
t7 strain: evolved PGCGROWTHCONDITIONS
time: 1 min post-infection PGCGROWTHCONDITIONS
cell culture PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
evolved 5min rep6 PGCGROWTHCONDITIONS
Fragmentation and reverse transcription of RNA with random primers was carried out using the NEB First Strand Synthesis Module (New England Biolabs). Second strand synthesis was done with the NEBNext Ultra Directional RNA Second Strand Synthesis Module (New England Biolabs), then purified with 1.7x AMPURE Bead XP (Beckman Coulter). DNA end repair was carried out with the NEBNext end repair module, dA-tailing used the NEBNext dA-Tailing Module and adapter ligation used the NEBNext Quick Ligation module (New England Biolabs). PCR amplification was carried out for 10 rounds of synthesis using the NEBNext High-Fidelity PCR Master Mix with NEBNext USER Enzyme (New England Biolabs), samples were purified with 1.0x AMPURE Bead XP (Beckman Coulter). Library quality was verified on a Bio-Analyzer DNA chip (Agilent). PGCGROWTHCONDITIONS
Genome_build: U00096.3 (E. coli K12) and NC_001604.1 (T7), excluding ribosomal genes, and with recoded gene 10 sequence (Bull, 2012, PMCID: PMC3457771) in place of wild-type sequence for analysis of recoded and evolved strains PGCGROWTHCONDITIONS
infection: T7 PGCGROWTHCONDITIONS
pseudoalignment and quantitation with kallisto v0.42.5 with parameters --single -l 450 -s 250 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using Trizol reagent (Thermo Fisher Scientific) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimitted text files contain TPM (transcripts per million) values for each sample PGCGROWTHCONDITIONS
t7 genotype: evolved, codon-deoptimized gene 10 PGCGROWTHCONDITIONS
t7 strain: evolved PGCGROWTHCONDITIONS
time: 5 min post-infection PGCGROWTHCONDITIONS
cell culture PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
evolved 5min rep8 PGCGROWTHCONDITIONS
Fragmentation and reverse transcription of RNA with random primers was carried out using the NEB First Strand Synthesis Module (New England Biolabs). Second strand synthesis was done with the NEBNext Ultra Directional RNA Second Strand Synthesis Module (New England Biolabs), then purified with 1.7x AMPURE Bead XP (Beckman Coulter). DNA end repair was carried out with the NEBNext end repair module, dA-tailing used the NEBNext dA-Tailing Module and adapter ligation used the NEBNext Quick Ligation module (New England Biolabs). PCR amplification was carried out for 10 rounds of synthesis using the NEBNext High-Fidelity PCR Master Mix with NEBNext USER Enzyme (New England Biolabs), samples were purified with 1.0x AMPURE Bead XP (Beckman Coulter). Library quality was verified on a Bio-Analyzer DNA chip (Agilent). PGCGROWTHCONDITIONS
Genome_build: U00096.3 (E. coli K12) and NC_001604.1 (T7), excluding ribosomal genes, and with recoded gene 10 sequence (Bull, 2012, PMCID: PMC3457771) in place of wild-type sequence for analysis of recoded and evolved strains PGCGROWTHCONDITIONS
infection: T7 PGCGROWTHCONDITIONS
pseudoalignment and quantitation with kallisto v0.42.5 with parameters --single -l 450 -s 250 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using Trizol reagent (Thermo Fisher Scientific) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimitted text files contain TPM (transcripts per million) values for each sample PGCGROWTHCONDITIONS
t7 genotype: evolved, codon-deoptimized gene 10 PGCGROWTHCONDITIONS
t7 strain: evolved PGCGROWTHCONDITIONS
time: 5 min post-infection PGCGROWTHCONDITIONS
cell culture PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
evolved 9min rep6 PGCGROWTHCONDITIONS
Fragmentation and reverse transcription of RNA with random primers was carried out using the NEB First Strand Synthesis Module (New England Biolabs). Second strand synthesis was done with the NEBNext Ultra Directional RNA Second Strand Synthesis Module (New England Biolabs), then purified with 1.7x AMPURE Bead XP (Beckman Coulter). DNA end repair was carried out with the NEBNext end repair module, dA-tailing used the NEBNext dA-Tailing Module and adapter ligation used the NEBNext Quick Ligation module (New England Biolabs). PCR amplification was carried out for 10 rounds of synthesis using the NEBNext High-Fidelity PCR Master Mix with NEBNext USER Enzyme (New England Biolabs), samples were purified with 1.0x AMPURE Bead XP (Beckman Coulter). Library quality was verified on a Bio-Analyzer DNA chip (Agilent). PGCGROWTHCONDITIONS
Genome_build: U00096.3 (E. coli K12) and NC_001604.1 (T7), excluding ribosomal genes, and with recoded gene 10 sequence (Bull, 2012, PMCID: PMC3457771) in place of wild-type sequence for analysis of recoded and evolved strains PGCGROWTHCONDITIONS
infection: T7 PGCGROWTHCONDITIONS
pseudoalignment and quantitation with kallisto v0.42.5 with parameters --single -l 450 -s 250 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using Trizol reagent (Thermo Fisher Scientific) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimitted text files contain TPM (transcripts per million) values for each sample PGCGROWTHCONDITIONS
t7 genotype: evolved, codon-deoptimized gene 10 PGCGROWTHCONDITIONS
t7 strain: evolved PGCGROWTHCONDITIONS
time: 9 min post-infection PGCGROWTHCONDITIONS
cell culture PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
evolved 9min rep7 PGCGROWTHCONDITIONS
Fragmentation and reverse transcription of RNA with random primers was carried out using the NEB First Strand Synthesis Module (New England Biolabs). Second strand synthesis was done with the NEBNext Ultra Directional RNA Second Strand Synthesis Module (New England Biolabs), then purified with 1.7x AMPURE Bead XP (Beckman Coulter). DNA end repair was carried out with the NEBNext end repair module, dA-tailing used the NEBNext dA-Tailing Module and adapter ligation used the NEBNext Quick Ligation module (New England Biolabs). PCR amplification was carried out for 10 rounds of synthesis using the NEBNext High-Fidelity PCR Master Mix with NEBNext USER Enzyme (New England Biolabs), samples were purified with 1.0x AMPURE Bead XP (Beckman Coulter). Library quality was verified on a Bio-Analyzer DNA chip (Agilent). PGCGROWTHCONDITIONS
Genome_build: U00096.3 (E. coli K12) and NC_001604.1 (T7), excluding ribosomal genes, and with recoded gene 10 sequence (Bull, 2012, PMCID: PMC3457771) in place of wild-type sequence for analysis of recoded and evolved strains PGCGROWTHCONDITIONS
infection: T7 PGCGROWTHCONDITIONS
pseudoalignment and quantitation with kallisto v0.42.5 with parameters --single -l 450 -s 250 PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
RNA was isolated using Trizol reagent (Thermo Fisher Scientific) PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: tab-delimitted text files contain TPM (transcripts per million) values for each sample PGCGROWTHCONDITIONS
t7 genotype: evolved, codon-deoptimized gene 10 PGCGROWTHCONDITIONS
t7 strain: evolved PGCGROWTHCONDITIONS
time: 9 min post-infection PGCGROWTHCONDITIONS
Adpater sequences were clipped with CutAdapt PGCGROWTHCONDITIONS
AR1-/AR2- rep 1 PGCGROWTHCONDITIONS
AR1-/AR2- PGCGROWTHCONDITIONS
Base calls were made using MiSeq Reporter v. 2.6.2.1 PGCGROWTHCONDITIONS
Cell pellets were lysed in Tissue and Cell lysis solution (EpiCentre) and proteinase K. RNA was isolated and DNase treated using the RNeasy Kit (Qiagen) using the manufacturer’s protocol. The amount of total RNA in each sample was quantified using the Qubit 2.0 Flurometer (Life Technologies) and quality was assessed using the RNA6000 Nano Chip on the Bioanalyzer 2100 (Agilent). PGCGROWTHCONDITIONS
Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS
Differential expression testing between sample groups was performed in Rstudio (v. 1.0.36) using DESeq2 (v.1.14.1) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: AR1-/AR2- PGCGROWTHCONDITIONS
growth phase: Late exponential/Early stationary (OD ~1.8) PGCGROWTHCONDITIONS
Low quality reads were trimmed with CutAdapt PGCGROWTHCONDITIONS
Mapped reads were counted using the Python package HTSeq (v. 0.6.1) using the following parameters; htseq-count -m union -r pos -i gene_name -a 10 PGCGROWTHCONDITIONS
media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depletion, fragmentation, reverse transcription, tagging, barcoding, limited cycle PCR (Illumina) PGCGROWTHCONDITIONS
ScriptSeq v2 Complete Kit (EpiCentre) PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma separated value files include log-fold changes and associated p-values for each comparison made PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: text files containing gene counts output by htseq-count PGCGROWTHCONDITIONS
The resulting reads were mapped to the reference genome of Escherichia coli str. K-12 substr. MG1655 using Tophat2 using the following parameters, --GTF --library type fr-secondstrand PGCGROWTHCONDITIONS
Adpater sequences were clipped with CutAdapt PGCGROWTHCONDITIONS
AR1-/AR2- rep 2 PGCGROWTHCONDITIONS
AR1-/AR2- PGCGROWTHCONDITIONS
Base calls were made using MiSeq Reporter v. 2.6.2.1 PGCGROWTHCONDITIONS
Cell pellets were lysed in Tissue and Cell lysis solution (EpiCentre) and proteinase K. RNA was isolated and DNase treated using the RNeasy Kit (Qiagen) using the manufacturer’s protocol. The amount of total RNA in each sample was quantified using the Qubit 2.0 Flurometer (Life Technologies) and quality was assessed using the RNA6000 Nano Chip on the Bioanalyzer 2100 (Agilent). PGCGROWTHCONDITIONS
Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS
Differential expression testing between sample groups was performed in Rstudio (v. 1.0.36) using DESeq2 (v.1.14.1) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: AR1-/AR2- PGCGROWTHCONDITIONS
growth phase: Late exponential/Early stationary (OD ~1.8) PGCGROWTHCONDITIONS
Low quality reads were trimmed with CutAdapt PGCGROWTHCONDITIONS
Mapped reads were counted using the Python package HTSeq (v. 0.6.1) using the following parameters; htseq-count -m union -r pos -i gene_name -a 10 PGCGROWTHCONDITIONS
media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depletion, fragmentation, reverse transcription, tagging, barcoding, limited cycle PCR (Illumina) PGCGROWTHCONDITIONS
ScriptSeq v2 Complete Kit (EpiCentre) PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma separated value files include log-fold changes and associated p-values for each comparison made PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: text files containing gene counts output by htseq-count PGCGROWTHCONDITIONS
The resulting reads were mapped to the reference genome of Escherichia coli str. K-12 substr. MG1655 using Tophat2 using the following parameters, --GTF --library type fr-secondstrand PGCGROWTHCONDITIONS
Adpater sequences were clipped with CutAdapt PGCGROWTHCONDITIONS
AR1-/AR2- rep 3 PGCGROWTHCONDITIONS
AR1-/AR2- PGCGROWTHCONDITIONS
Base calls were made using MiSeq Reporter v. 2.6.2.1 PGCGROWTHCONDITIONS
Cell pellets were lysed in Tissue and Cell lysis solution (EpiCentre) and proteinase K. RNA was isolated and DNase treated using the RNeasy Kit (Qiagen) using the manufacturer’s protocol. The amount of total RNA in each sample was quantified using the Qubit 2.0 Flurometer (Life Technologies) and quality was assessed using the RNA6000 Nano Chip on the Bioanalyzer 2100 (Agilent). PGCGROWTHCONDITIONS
Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS
Differential expression testing between sample groups was performed in Rstudio (v. 1.0.36) using DESeq2 (v.1.14.1) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: AR1-/AR2- PGCGROWTHCONDITIONS
growth phase: Late exponential/Early stationary (OD ~1.8) PGCGROWTHCONDITIONS
Low quality reads were trimmed with CutAdapt PGCGROWTHCONDITIONS
Mapped reads were counted using the Python package HTSeq (v. 0.6.1) using the following parameters; htseq-count -m union -r pos -i gene_name -a 10 PGCGROWTHCONDITIONS
media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depletion, fragmentation, reverse transcription, tagging, barcoding, limited cycle PCR (Illumina) PGCGROWTHCONDITIONS
ScriptSeq v2 Complete Kit (EpiCentre) PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma separated value files include log-fold changes and associated p-values for each comparison made PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: text files containing gene counts output by htseq-count PGCGROWTHCONDITIONS
The resulting reads were mapped to the reference genome of Escherichia coli str. K-12 substr. MG1655 using Tophat2 using the following parameters, --GTF --library type fr-secondstrand PGCGROWTHCONDITIONS
Adpater sequences were clipped with CutAdapt PGCGROWTHCONDITIONS
Base calls were made using MiSeq Reporter v. 2.6.2.1 PGCGROWTHCONDITIONS
Cell pellets were lysed in Tissue and Cell lysis solution (EpiCentre) and proteinase K. RNA was isolated and DNase treated using the RNeasy Kit (Qiagen) using the manufacturer’s protocol. The amount of total RNA in each sample was quantified using the Qubit 2.0 Flurometer (Life Technologies) and quality was assessed using the RNA6000 Nano Chip on the Bioanalyzer 2100 (Agilent). PGCGROWTHCONDITIONS
Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS
Differential expression testing between sample groups was performed in Rstudio (v. 1.0.36) using DESeq2 (v.1.14.1) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: WT PGCGROWTHCONDITIONS
growth phase: Late exponential/Early stationary (OD ~1.8) PGCGROWTHCONDITIONS
Low quality reads were trimmed with CutAdapt PGCGROWTHCONDITIONS
Mapped reads were counted using the Python package HTSeq (v. 0.6.1) using the following parameters; htseq-count -m union -r pos -i gene_name -a 10 PGCGROWTHCONDITIONS
media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depletion, fragmentation, reverse transcription, tagging, barcoding, limited cycle PCR (Illumina) PGCGROWTHCONDITIONS
ScriptSeq v2 Complete Kit (EpiCentre) PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma separated value files include log-fold changes and associated p-values for each comparison made PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: text files containing gene counts output by htseq-count PGCGROWTHCONDITIONS
The resulting reads were mapped to the reference genome of Escherichia coli str. K-12 substr. MG1655 using Tophat2 using the following parameters, --GTF --library type fr-secondstrand PGCGROWTHCONDITIONS
WT rep 1 PGCGROWTHCONDITIONS
WT PGCGROWTHCONDITIONS
Adpater sequences were clipped with CutAdapt PGCGROWTHCONDITIONS
Base calls were made using MiSeq Reporter v. 2.6.2.1 PGCGROWTHCONDITIONS
Cell pellets were lysed in Tissue and Cell lysis solution (EpiCentre) and proteinase K. RNA was isolated and DNase treated using the RNeasy Kit (Qiagen) using the manufacturer’s protocol. The amount of total RNA in each sample was quantified using the Qubit 2.0 Flurometer (Life Technologies) and quality was assessed using the RNA6000 Nano Chip on the Bioanalyzer 2100 (Agilent). PGCGROWTHCONDITIONS
Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS
Differential expression testing between sample groups was performed in Rstudio (v. 1.0.36) using DESeq2 (v.1.14.1) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: WT PGCGROWTHCONDITIONS
growth phase: Late exponential/Early stationary (OD ~1.8) PGCGROWTHCONDITIONS
Low quality reads were trimmed with CutAdapt PGCGROWTHCONDITIONS
Mapped reads were counted using the Python package HTSeq (v. 0.6.1) using the following parameters; htseq-count -m union -r pos -i gene_name -a 10 PGCGROWTHCONDITIONS
media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depletion, fragmentation, reverse transcription, tagging, barcoding, limited cycle PCR (Illumina) PGCGROWTHCONDITIONS
ScriptSeq v2 Complete Kit (EpiCentre) PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma separated value files include log-fold changes and associated p-values for each comparison made PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: text files containing gene counts output by htseq-count PGCGROWTHCONDITIONS
The resulting reads were mapped to the reference genome of Escherichia coli str. K-12 substr. MG1655 using Tophat2 using the following parameters, --GTF --library type fr-secondstrand PGCGROWTHCONDITIONS
WT rep 2 PGCGROWTHCONDITIONS
WT PGCGROWTHCONDITIONS
Adpater sequences were clipped with CutAdapt PGCGROWTHCONDITIONS
Base calls were made using MiSeq Reporter v. 2.6.2.1 PGCGROWTHCONDITIONS
Cell pellets were lysed in Tissue and Cell lysis solution (EpiCentre) and proteinase K. RNA was isolated and DNase treated using the RNeasy Kit (Qiagen) using the manufacturer’s protocol. The amount of total RNA in each sample was quantified using the Qubit 2.0 Flurometer (Life Technologies) and quality was assessed using the RNA6000 Nano Chip on the Bioanalyzer 2100 (Agilent). PGCGROWTHCONDITIONS
Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS
Differential expression testing between sample groups was performed in Rstudio (v. 1.0.36) using DESeq2 (v.1.14.1) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: WT PGCGROWTHCONDITIONS
growth phase: Late exponential/Early stationary (OD ~1.8) PGCGROWTHCONDITIONS
Low quality reads were trimmed with CutAdapt PGCGROWTHCONDITIONS
Mapped reads were counted using the Python package HTSeq (v. 0.6.1) using the following parameters; htseq-count -m union -r pos -i gene_name -a 10 PGCGROWTHCONDITIONS
media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depletion, fragmentation, reverse transcription, tagging, barcoding, limited cycle PCR (Illumina) PGCGROWTHCONDITIONS
ScriptSeq v2 Complete Kit (EpiCentre) PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma separated value files include log-fold changes and associated p-values for each comparison made PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: text files containing gene counts output by htseq-count PGCGROWTHCONDITIONS
The resulting reads were mapped to the reference genome of Escherichia coli str. K-12 substr. MG1655 using Tophat2 using the following parameters, --GTF --library type fr-secondstrand PGCGROWTHCONDITIONS
WT rep 3 PGCGROWTHCONDITIONS
WT PGCGROWTHCONDITIONS
Adpater sequences were clipped with CutAdapt PGCGROWTHCONDITIONS
Base calls were made using MiSeq Reporter v. 2.6.2.1 PGCGROWTHCONDITIONS
Cell pellets were lysed in Tissue and Cell lysis solution (EpiCentre) and proteinase K. RNA was isolated and DNase treated using the RNeasy Kit (Qiagen) using the manufacturer’s protocol. The amount of total RNA in each sample was quantified using the Qubit 2.0 Flurometer (Life Technologies) and quality was assessed using the RNA6000 Nano Chip on the Bioanalyzer 2100 (Agilent). PGCGROWTHCONDITIONS
Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS
Differential expression testing between sample groups was performed in Rstudio (v. 1.0.36) using DESeq2 (v.1.14.1) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: K100Q PGCGROWTHCONDITIONS
growth phase: Late exponential/Early stationary (OD ~1.8) PGCGROWTHCONDITIONS
K100Q rep 1 PGCGROWTHCONDITIONS
K100Q PGCGROWTHCONDITIONS
Low quality reads were trimmed with CutAdapt PGCGROWTHCONDITIONS
Mapped reads were counted using the Python package HTSeq (v. 0.6.1) using the following parameters; htseq-count -m union -r pos -i gene_name -a 10 PGCGROWTHCONDITIONS
media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depletion, fragmentation, reverse transcription, tagging, barcoding, limited cycle PCR (Illumina) PGCGROWTHCONDITIONS
ScriptSeq v2 Complete Kit (EpiCentre) PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma separated value files include log-fold changes and associated p-values for each comparison made PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: text files containing gene counts output by htseq-count PGCGROWTHCONDITIONS
The resulting reads were mapped to the reference genome of Escherichia coli str. K-12 substr. MG1655 using Tophat2 using the following parameters, --GTF --library type fr-secondstrand PGCGROWTHCONDITIONS
Adpater sequences were clipped with CutAdapt PGCGROWTHCONDITIONS
Base calls were made using MiSeq Reporter v. 2.6.2.1 PGCGROWTHCONDITIONS
Cell pellets were lysed in Tissue and Cell lysis solution (EpiCentre) and proteinase K. RNA was isolated and DNase treated using the RNeasy Kit (Qiagen) using the manufacturer’s protocol. The amount of total RNA in each sample was quantified using the Qubit 2.0 Flurometer (Life Technologies) and quality was assessed using the RNA6000 Nano Chip on the Bioanalyzer 2100 (Agilent). PGCGROWTHCONDITIONS
Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS
Differential expression testing between sample groups was performed in Rstudio (v. 1.0.36) using DESeq2 (v.1.14.1) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: K100Q PGCGROWTHCONDITIONS
growth phase: Late exponential/Early stationary (OD ~1.8) PGCGROWTHCONDITIONS
K100Q rep 3 PGCGROWTHCONDITIONS
K100Q PGCGROWTHCONDITIONS
Low quality reads were trimmed with CutAdapt PGCGROWTHCONDITIONS
Mapped reads were counted using the Python package HTSeq (v. 0.6.1) using the following parameters; htseq-count -m union -r pos -i gene_name -a 10 PGCGROWTHCONDITIONS
media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depletion, fragmentation, reverse transcription, tagging, barcoding, limited cycle PCR (Illumina) PGCGROWTHCONDITIONS
ScriptSeq v2 Complete Kit (EpiCentre) PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma separated value files include log-fold changes and associated p-values for each comparison made PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: text files containing gene counts output by htseq-count PGCGROWTHCONDITIONS
The resulting reads were mapped to the reference genome of Escherichia coli str. K-12 substr. MG1655 using Tophat2 using the following parameters, --GTF --library type fr-secondstrand PGCGROWTHCONDITIONS
Adpater sequences were clipped with CutAdapt PGCGROWTHCONDITIONS
Base calls were made using MiSeq Reporter v. 2.6.2.1 PGCGROWTHCONDITIONS
Cell pellets were lysed in Tissue and Cell lysis solution (EpiCentre) and proteinase K. RNA was isolated and DNase treated using the RNeasy Kit (Qiagen) using the manufacturer’s protocol. The amount of total RNA in each sample was quantified using the Qubit 2.0 Flurometer (Life Technologies) and quality was assessed using the RNA6000 Nano Chip on the Bioanalyzer 2100 (Agilent). PGCGROWTHCONDITIONS
Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS
Differential expression testing between sample groups was performed in Rstudio (v. 1.0.36) using DESeq2 (v.1.14.1) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: K100R PGCGROWTHCONDITIONS
growth phase: Late exponential/Early stationary (OD ~1.8) PGCGROWTHCONDITIONS
K100R rep 1 PGCGROWTHCONDITIONS
K100R PGCGROWTHCONDITIONS
Low quality reads were trimmed with CutAdapt PGCGROWTHCONDITIONS
Mapped reads were counted using the Python package HTSeq (v. 0.6.1) using the following parameters; htseq-count -m union -r pos -i gene_name -a 10 PGCGROWTHCONDITIONS
media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depletion, fragmentation, reverse transcription, tagging, barcoding, limited cycle PCR (Illumina) PGCGROWTHCONDITIONS
ScriptSeq v2 Complete Kit (EpiCentre) PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma separated value files include log-fold changes and associated p-values for each comparison made PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: text files containing gene counts output by htseq-count PGCGROWTHCONDITIONS
The resulting reads were mapped to the reference genome of Escherichia coli str. K-12 substr. MG1655 using Tophat2 using the following parameters, --GTF --library type fr-secondstrand PGCGROWTHCONDITIONS
Adpater sequences were clipped with CutAdapt PGCGROWTHCONDITIONS
Base calls were made using MiSeq Reporter v. 2.6.2.1 PGCGROWTHCONDITIONS
Cell pellets were lysed in Tissue and Cell lysis solution (EpiCentre) and proteinase K. RNA was isolated and DNase treated using the RNeasy Kit (Qiagen) using the manufacturer’s protocol. The amount of total RNA in each sample was quantified using the Qubit 2.0 Flurometer (Life Technologies) and quality was assessed using the RNA6000 Nano Chip on the Bioanalyzer 2100 (Agilent). PGCGROWTHCONDITIONS
Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS
Differential expression testing between sample groups was performed in Rstudio (v. 1.0.36) using DESeq2 (v.1.14.1) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: K100R PGCGROWTHCONDITIONS
growth phase: Late exponential/Early stationary (OD ~1.8) PGCGROWTHCONDITIONS
K100R rep 2 PGCGROWTHCONDITIONS
K100R PGCGROWTHCONDITIONS
Low quality reads were trimmed with CutAdapt PGCGROWTHCONDITIONS
Mapped reads were counted using the Python package HTSeq (v. 0.6.1) using the following parameters; htseq-count -m union -r pos -i gene_name -a 10 PGCGROWTHCONDITIONS
media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depletion, fragmentation, reverse transcription, tagging, barcoding, limited cycle PCR (Illumina) PGCGROWTHCONDITIONS
ScriptSeq v2 Complete Kit (EpiCentre) PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma separated value files include log-fold changes and associated p-values for each comparison made PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: text files containing gene counts output by htseq-count PGCGROWTHCONDITIONS
The resulting reads were mapped to the reference genome of Escherichia coli str. K-12 substr. MG1655 using Tophat2 using the following parameters, --GTF --library type fr-secondstrand PGCGROWTHCONDITIONS
Adpater sequences were clipped with CutAdapt PGCGROWTHCONDITIONS
Base calls were made using MiSeq Reporter v. 2.6.2.1 PGCGROWTHCONDITIONS
Cell pellets were lysed in Tissue and Cell lysis solution (EpiCentre) and proteinase K. RNA was isolated and DNase treated using the RNeasy Kit (Qiagen) using the manufacturer’s protocol. The amount of total RNA in each sample was quantified using the Qubit 2.0 Flurometer (Life Technologies) and quality was assessed using the RNA6000 Nano Chip on the Bioanalyzer 2100 (Agilent). PGCGROWTHCONDITIONS
Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS
Differential expression testing between sample groups was performed in Rstudio (v. 1.0.36) using DESeq2 (v.1.14.1) PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
genotype/variation: K100R PGCGROWTHCONDITIONS
growth phase: Late exponential/Early stationary (OD ~1.8) PGCGROWTHCONDITIONS
K100R rep 3 PGCGROWTHCONDITIONS
K100R PGCGROWTHCONDITIONS
Low quality reads were trimmed with CutAdapt PGCGROWTHCONDITIONS
Mapped reads were counted using the Python package HTSeq (v. 0.6.1) using the following parameters; htseq-count -m union -r pos -i gene_name -a 10 PGCGROWTHCONDITIONS
media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
rRNA depletion, fragmentation, reverse transcription, tagging, barcoding, limited cycle PCR (Illumina) PGCGROWTHCONDITIONS
ScriptSeq v2 Complete Kit (EpiCentre) PGCGROWTHCONDITIONS
strain: K-12 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: Comma separated value files include log-fold changes and associated p-values for each comparison made PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: text files containing gene counts output by htseq-count PGCGROWTHCONDITIONS
The resulting reads were mapped to the reference genome of Escherichia coli str. K-12 substr. MG1655 using Tophat2 using the following parameters, --GTF --library type fr-secondstrand PGCGROWTHCONDITIONS
50 bp single-end reads, were mapped to the genome with using bowtie2(Langmead and Salzberg, 2012) using default parameters. Alignments with bowtie2 mapping quality values lower than 40 were not retained for further analysis, leaving 128,413,654 and 76,508,335 reads. PGCGROWTHCONDITIONS
E. coli 3' RACE Rep1 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
In order to distinguish between 3’ ends of transient products of RNA metabolism and stable 3’ ends, we developed an algorithm to call coverage peaks. The algorithm will be discussed in detail in an upcoming manuscript, and the scripts used are available upon request from the authors. In short, positions in the E. coli genome were considered in descending order of coverage and assigned a p-value based on a Poisson distribution parameterized by the mean coverage of all covered bases in the genome. Peaks were rejected if their p-values exceeded 1e-4 or if there existed a >10-bp window containing the peak in which all positions were within 2-fold coverage of the peak position. Parameters were chosen based on analysis of annotated 3’ ends as well as qualitative analysis of peaks. This resulted in 20,019 peaks. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K12 MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BIGWIG file containing coverage tracks from 3' RACE data PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: GFF file containing 3' end annotations PGCGROWTHCONDITIONS
total DNaseI treated RNA was depleted of ribosomal RNA using the Ribo-Zero™ RNA removal kit for Gram-negative bacteria (Epicentre). A 3' RNA adapter, based on the Illumina multiplexing adapter sequence (Oligonucleotide sequences © 2007-2014 Illumina, Inc. All rights reserved) blocked at the 3' end with an inverted dT (5'-GAUCGGAAGAGCACACGUCU[idT]-3'), was phosphorylated at the 5' end using T4 PNK (New England Biolabs) per the manufacturer’s protocol. The 3' RNA adapter was ligated to the 3' ends of the rRNA depleted RNA using T4 RNA ligase I (New England Biolabs). 1.5 mg of RNA was incubated at 20°C for 6 hours in 1X T4 RNA ligase reaction buffer with 1 mM ATP, 30 µM 3' RNA adapter, 10 % DMSO, 10 U of T4 RNA ligase I, and 40 U of RNasin (Promega) in a 20 ml reaction. RNA was then fragmented in equivalents of 100 ng using the RNA fragmentation reagents (Ambion®) per the manufacturer’s protocol at 70°C for 3 min and subsequently phosphorylated at the 5' ends using T4 PNK (New England Biolabs) per the manufacturer’s protocol to allow for ligation of the 5' adapter. RNA was size-selected (≈ 150-300 nt) and purified over a denaturing 8 % polyacrylamide/8 M urea/TBE gel. Gel slices were incubated in RNA elution buffer (10 mM Tris-HCl, pH 7.5, 2 mM EDTA, 0.1 % SDS, 0.3 M NaOAc) with vigorous shaking at 4°C overnight. The supernatant was subsequently ethanol precipitated using glycogen as a carrier molecule. The Illumina small RNA 5' adapter (5'-GUUCAGAGUUCUACAGUCCGACGAUC-3') was ligated to the RNA as described before except the concentration of the adapter was 52 mM and 20 U of T4 RNA ligase I was used in total volume of 25 µl. The ligated RNAs were size-selected (≈ 200-300 nt) and gel-purified over a denaturing 8 % polyacrylamide/8 M urea/TBE gel (as described above). The di-tagged RNA libraries were reverse-transcribed with SuperScript®II reverse transcriptase (Invitrogen) using random nonamers per the manufacturer’s protocol. RNA was removed using RNase H (Promega) per the manufacturer’s protocol and cDNA was amplified in PCR carried out using Phusion® High-Fidelity Polymerase (New England Biolabs). cDNA was amplified with modified designed Illumina-compatible PCR primers (3’ library Forward 5’-CAAGCAGAAGACGGCATACGACAGGTTCAGAGTTCTACAGTCCGA-3’; Reverse 5’-AATGATACGGCGACCACCGAGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-3’) by 18 cycles of PCR. The products were purified using Agencourt AMPure XP beads (Beckman) and analyzed on an Agilent 2100 Bioanalyzer. 3’ end enriched cDNA libraries were sequenced on individual Genome Analyzer IIx lanes (36 bp, single-end) or on HiSeq 2000 lanes (50 bp, single-end) using primer based on Illumina Multiplexing Read 2 Sequencing Primer (5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-3’) at the CSF NGS unit http://csf.ac.at/. PGCGROWTHCONDITIONS
Total RNA was isolated using the hot phenol method as described in (Lybecker et al., 2014). PGCGROWTHCONDITIONS
50 bp single-end reads, were mapped to the genome with using bowtie2(Langmead and Salzberg, 2012) using default parameters. Alignments with bowtie2 mapping quality values lower than 40 were not retained for further analysis, leaving 128,413,654 and 76,508,335 reads. PGCGROWTHCONDITIONS
E. coli 3' RACE Rep2 PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
In order to distinguish between 3’ ends of transient products of RNA metabolism and stable 3’ ends, we developed an algorithm to call coverage peaks. The algorithm will be discussed in detail in an upcoming manuscript, and the scripts used are available upon request from the authors. In short, positions in the E. coli genome were considered in descending order of coverage and assigned a p-value based on a Poisson distribution parameterized by the mean coverage of all covered bases in the genome. Peaks were rejected if their p-values exceeded 1e-4 or if there existed a >10-bp window containing the peak in which all positions were within 2-fold coverage of the peak position. Parameters were chosen based on analysis of annotated 3’ ends as well as qualitative analysis of peaks. This resulted in 20,019 peaks. PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: K12 MG1655 PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: BIGWIG file containing coverage tracks from 3' RACE data PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: GFF file containing 3' end annotations PGCGROWTHCONDITIONS
total DNaseI treated RNA was depleted of ribosomal RNA using the Ribo-Zero™ RNA removal kit for Gram-negative bacteria (Epicentre). A 3' RNA adapter, based on the Illumina multiplexing adapter sequence (Oligonucleotide sequences © 2007-2014 Illumina, Inc. All rights reserved) blocked at the 3' end with an inverted dT (5'-GAUCGGAAGAGCACACGUCU[idT]-3'), was phosphorylated at the 5' end using T4 PNK (New England Biolabs) per the manufacturer’s protocol. The 3' RNA adapter was ligated to the 3' ends of the rRNA depleted RNA using T4 RNA ligase I (New England Biolabs). 1.5 mg of RNA was incubated at 20°C for 6 hours in 1X T4 RNA ligase reaction buffer with 1 mM ATP, 30 µM 3' RNA adapter, 10 % DMSO, 10 U of T4 RNA ligase I, and 40 U of RNasin (Promega) in a 20 ml reaction. RNA was then fragmented in equivalents of 100 ng using the RNA fragmentation reagents (Ambion®) per the manufacturer’s protocol at 70°C for 3 min and subsequently phosphorylated at the 5' ends using T4 PNK (New England Biolabs) per the manufacturer’s protocol to allow for ligation of the 5' adapter. RNA was size-selected (≈ 150-300 nt) and purified over a denaturing 8 % polyacrylamide/8 M urea/TBE gel. Gel slices were incubated in RNA elution buffer (10 mM Tris-HCl, pH 7.5, 2 mM EDTA, 0.1 % SDS, 0.3 M NaOAc) with vigorous shaking at 4°C overnight. The supernatant was subsequently ethanol precipitated using glycogen as a carrier molecule. The Illumina small RNA 5' adapter (5'-GUUCAGAGUUCUACAGUCCGACGAUC-3') was ligated to the RNA as described before except the concentration of the adapter was 52 mM and 20 U of T4 RNA ligase I was used in total volume of 25 µl. The ligated RNAs were size-selected (≈ 200-300 nt) and gel-purified over a denaturing 8 % polyacrylamide/8 M urea/TBE gel (as described above). The di-tagged RNA libraries were reverse-transcribed with SuperScript®II reverse transcriptase (Invitrogen) using random nonamers per the manufacturer’s protocol. RNA was removed using RNase H (Promega) per the manufacturer’s protocol and cDNA was amplified in PCR carried out using Phusion® High-Fidelity Polymerase (New England Biolabs). cDNA was amplified with modified designed Illumina-compatible PCR primers (3’ library Forward 5’-CAAGCAGAAGACGGCATACGACAGGTTCAGAGTTCTACAGTCCGA-3’; Reverse 5’-AATGATACGGCGACCACCGAGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-3’) by 18 cycles of PCR. The products were purified using Agencourt AMPure XP beads (Beckman) and analyzed on an Agilent 2100 Bioanalyzer. 3’ end enriched cDNA libraries were sequenced on individual Genome Analyzer IIx lanes (36 bp, single-end) or on HiSeq 2000 lanes (50 bp, single-end) using primer based on Illumina Multiplexing Read 2 Sequencing Primer (5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-3’) at the CSF NGS unit http://csf.ac.at/. PGCGROWTHCONDITIONS
Total RNA was isolated using the hot phenol method as described in (Lybecker et al., 2014). PGCGROWTHCONDITIONS
0x58 replicate 2 state 1 (IPTG-/aTc-/Ara-) PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
0x58 replicate 2 state 2 (IPTG+/aTc-/Ara-) PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
0x58 replicate 2 state 3 (IPTG-/aTc+/Ara-) PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
0x58 replicate 2 state 4 (IPTG+/aTc+/Ara-) PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
0x58 replicate 2 state 5 (IPTG-/aTc-/Ara+) PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
0x58 replicate 2 state 6 (IPTG+/aTc-/Ara+) PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
0x58 replicate 2 state 7 (IPTG-/aTc+/Ara+) PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
0x58 replicate 2 state 8 (IPTG+/aTc+/Ara+) PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
0x58 replicate 3 state 1 (IPTG-/aTc-/Ara-) PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
0x58 replicate 3 state 2 (IPTG+/aTc-/Ara-) PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
0x58 replicate 3 state 3 (IPTG-/aTc+/Ara-) PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
0x58 replicate 3 state 4 (IPTG+/aTc+/Ara-) PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
0x58 replicate 3 state 5 (IPTG-/aTc-/Ara+) PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
0x58 replicate 3 state 6 (IPTG+/aTc-/Ara+) PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
0x58 replicate 3 state 7 (IPTG-/aTc+/Ara+) PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
0x58 replicate 3 state 8 (IPTG+/aTc+/Ara+) PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
Control pAN1201 replicate 1 (IPTG-/aTc-/Ara-) PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS
Control pAN1201 replicate 2 (IPTG-/aTc-/Ara-) PGCGROWTHCONDITIONS
Culture grown in 14 ml tube PGCGROWTHCONDITIONS
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples. PGCGROWTHCONDITIONS
Escherichia coli PGCGROWTHCONDITIONS
Genome_build: NC_010473.1 PGCGROWTHCONDITIONS
Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6. PGCGROWTHCONDITIONS
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'. PGCGROWTHCONDITIONS
Reads mapped to reference using BWA versiopn 0.7.4 with default settings PGCGROWTHCONDITIONS
RNA-Seq PGCGROWTHCONDITIONS
strain: NEB 10-beta PGCGROWTHCONDITIONS
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016. PGCGROWTHCONDITIONS
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units. PGCGROWTHCONDITIONS