SRR9919224	GSE135516	GSM4013462	GPL24377	PMID_31651953	WT_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	data_processing	The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20; PGCGROWTHCONDITIONS
SRR9919224	GSE135516	GSM4013462	GPL24377	PMID_31651953	WT_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	data_processing	Sequence reads generated from RNA-Seq were mapped onto the reference genome (NC_000913.2) using bowtie with default options to generate SAM output files PGCGROWTHCONDITIONS
SRR9919224	GSE135516	GSM4013462	GPL24377	PMID_31651953	WT_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	data_processing	Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package with strand inversion for the dUTP protocol and strict intersection mode PGCGROWTHCONDITIONS
SRR9919224	GSE135516	GSM4013462	GPL24377	PMID_31651953	WT_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	data_processing	Estimated the dispersion of each gene using DESeq2 PGCGROWTHCONDITIONS
SRR9919224	GSE135516	GSM4013462	GPL24377	PMID_31651953	WT_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	data_processing	Transcript per Million (TPM) were calculated by DESeq2 PGCGROWTHCONDITIONS
SRR9919224	GSE135516	GSM4013462	GPL24377	PMID_31651953	WT_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	data_processing	Genome_build: E.coli genome(NC_000913.3) PGCGROWTHCONDITIONS
SRR9919224	GSE135516	GSM4013462	GPL24377	PMID_31651953	WT_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	data_processing	Supplementary_files_format_and_content: csv file includes TPM values for each Sample PGCGROWTHCONDITIONS
SRR9919224	GSE135516	GSM4013462	GPL24377	PMID_31651953	WT_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	extract_protocol	KAPA Stranded RNA-Seq Kit PGCGROWTHCONDITIONS
SRR9919224	GSE135516	GSM4013462	GPL24377	PMID_31651953	WT_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	growth_protocol	Glycerol stocks of E. coli strains were inoculated into M9 minimal media with glucose as 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). PGCGROWTHCONDITIONS
SRR9919224	GSE135516	GSM4013462	GPL24377	PMID_31651953	WT_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	organism	Escherichia coli K-12 PGCGROWTHCONDITIONS
SRR9919224	GSE135516	GSM4013462	GPL24377	PMID_31651953	WT_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	source_name	WT_mid-log phase bacteria culture PGCGROWTHCONDITIONS
SRR9919224	GSE135516	GSM4013462	GPL24377	PMID_31651953	WT_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR9919224	GSE135516	GSM4013462	GPL24377	PMID_31651953	WT_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	strain: MG1655 PGCGROWTHCONDITIONS
SRR9919224	GSE135516	GSM4013462	GPL24377	PMID_31651953	WT_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS
SRR9919224	GSE135516	GSM4013462	GPL24377	PMID_31651953	WT_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	growth_protocol	Glycerol stocks of E. coli strains were inoculated into M9 minimal media with glucose as 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). PGCGROWTHCONDITIONS
SRR9919224	GSE135516	GSM4013462	GPL24377	PMID_31651953	WT_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	organism	Escherichia coli K-12 PGCGROWTHCONDITIONS
SRR9919224	GSE135516	GSM4013462	GPL24377	PMID_31651953	WT_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	source_name	WT_mid-log phase bacteria culture PGCGROWTHCONDITIONS
SRR9919224	GSE135516	GSM4013462	GPL24377	PMID_31651953	WT_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	contact_name	Amitesh,,Anand PGCGROWTHCONDITIONS