SRR8587786	GSE126710	GSM3611668	GPL26204	PMID_31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	data_processing	quality trimming (cut-off of 20) and adapter removal using cutadapt 1.15 PGCGROWTHCONDITIONS
SRR8587786	GSE126710	GSM3611668	GPL26204	PMID_31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	data_processing	generattion of reverse complement reads using FASTX 0.0.14 PGCGROWTHCONDITIONS
SRR8587786	GSE126710	GSM3611668	GPL26204	PMID_31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	data_processing	poly A-tail removal using READemption 0.4.3 PGCGROWTHCONDITIONS
SRR8587786	GSE126710	GSM3611668	GPL26204	PMID_31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	data_processing	mapping of reads to E. coli MG1655, φO104 and φPA8 genomes using READemption 0.4.3 and segemehl 0.2.0 PGCGROWTHCONDITIONS
SRR8587786	GSE126710	GSM3611668	GPL26204	PMID_31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	data_processing	gene wise quantification (quantification of the number of reads overlapping with the locations of the annotation entries) using READemption 0.4.3 PGCGROWTHCONDITIONS
SRR8587786	GSE126710	GSM3611668	GPL26204	PMID_31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	data_processing	differential gene expression analysis based on the gene wise qunatification for  E. coli MG1655 annotation using READemption 0.4.3 and DESeq2 1.16.1 PGCGROWTHCONDITIONS
SRR8587786	GSE126710	GSM3611668	GPL26204	PMID_31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	data_processing	Genome_build: E. coli MG1655 (U00096.3), φPA8 (KP682374.1) and φO104 (3256115 to 3317011 from NC_018658.1) PGCGROWTHCONDITIONS
SRR8587786	GSE126710	GSM3611668	GPL26204	PMID_31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	data_processing	Supplementary_files_format_and_content: csv file of the gene wise quantification data used for DESeq2 analysis PGCGROWTHCONDITIONS
SRR8587786	GSE126710	GSM3611668	GPL26204	PMID_31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	extract_protocol	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 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). The RNA preparations were further treated with RiboZero (Illumina) and the concentration of the samples was determined with Qubit. PGCGROWTHCONDITIONS
SRR8587786	GSE126710	GSM3611668	GPL26204	PMID_31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	extract_protocol	cDNA libraries for the Illumina sequencing platform were constructed using NEBNext Ultra Directional RNA Library Kit following the manufacturer[linebreak]s instructions. PGCGROWTHCONDITIONS
SRR8587786	GSE126710	GSM3611668	GPL26204	PMID_31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	growth_protocol	Overnight cultures were diluted till OD600 of 0.005 in LB medium (10 g/L tryptone, 5 g/L yeast extract, 5 g/L NaCl) and cells were grown at 37oC, 180 rpm to an OD600 of 0.4 - 0.6. PGCGROWTHCONDITIONS
SRR8587786	GSE126710	GSM3611668	GPL26204	PMID_31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	organism	Escherichia coli K-12 PGCGROWTHCONDITIONS
SRR8587786	GSE126710	GSM3611668	GPL26204	PMID_31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	source_name	MG1655 PGCGROWTHCONDITIONS
SRR8587786	GSE126710	GSM3611668	GPL26204	PMID_31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	treatment_protocol	After the treatment with stop solution (5 % phenol/95 % ethanol), cells pellets were immediately lysed with cell lysis buffer (85 mg/mL lysozyme in TE buffer, pH 8). One ml of Trizol reagent was added and samples were stored at -20C till the RNA isolation protocol was resumed. PGCGROWTHCONDITIONS
SRR8587786	GSE126710	GSM3611668	GPL26204	PMID_31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR8587786	GSE126710	GSM3611668	GPL26204	PMID_31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	characteristics	strain background: MG1655 PGCGROWTHCONDITIONS
SRR8587786	GSE126710	GSM3611668	GPL26204	PMID_31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	characteristics	genotype/variation: naive (wild type) PGCGROWTHCONDITIONS
SRR8587786	GSE126710	GSM3611668	GPL26204	PMID_31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	characteristics	growth phase: exponentially growing cells PGCGROWTHCONDITIONS
SRR8587786	GSE126710	GSM3611668	GPL26204	PMID_31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	growth_protocol	Overnight cultures were diluted till OD600 of 0.005 in LB medium (10 g/L tryptone, 5 g/L yeast extract, 5 g/L NaCl) and cells were grown at 37oC, 180 rpm to an OD600 of 0.4 - 0.6. PGCGROWTHCONDITIONS
SRR8587786	GSE126710	GSM3611668	GPL26204	PMID_31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	organism	Escherichia coli K-12 PGCGROWTHCONDITIONS
SRR8587786	GSE126710	GSM3611668	GPL26204	PMID_31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	source_name	MG1655 PGCGROWTHCONDITIONS
SRR8587786	GSE126710	GSM3611668	GPL26204	PMID_31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	treatment_protocol	After the treatment with stop solution (5 % phenol/95 % ethanol), cells pellets were immediately lysed with cell lysis buffer (85 mg/mL lysozyme in TE buffer, pH 8). One ml of Trizol reagent was added and samples were stored at -20C till the RNA isolation protocol was resumed. PGCGROWTHCONDITIONS
SRR8587786	GSE126710	GSM3611668	GPL26204	PMID_31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	contact_name	Petya,,Berger PGCGROWTHCONDITIONS