SRR7057988	GSE111094	GSM3108937	GPL24659	PMID_33149261	WT-high-ph rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	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
SRR7057988	GSE111094	GSM3108937	GPL24659	PMID_33149261	WT-high-ph rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Sequence reads generated from RNA-seq were mapped onto the reference genome (NC_000913.2) using bowtie with the maximum insert size of 1000 bp, and 2 maximum mismatches after trimming 3 bp at 3’ ends PGCGROWTHCONDITIONS
SRR7057988	GSE111094	GSM3108937	GPL24659	PMID_33149261	WT-high-ph rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	data_processing	SAM files generated from bowtie, then, were then used for Cufflinks (http://cufflinks.cbcb.umd.edu/) to calculate fragments per kilobase of exon per million fragments (FPKM). PGCGROWTHCONDITIONS
SRR7057988	GSE111094	GSM3108937	GPL24659	PMID_33149261	WT-high-ph rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Cufflinks was run with default options with the library type of dUTP RNA-seq and the default normalization method (classic-fpkm) PGCGROWTHCONDITIONS
SRR7057988	GSE111094	GSM3108937	GPL24659	PMID_33149261	WT-high-ph rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Genome_build: reference genome (NC_000913.2) PGCGROWTHCONDITIONS
SRR7057988	GSE111094	GSM3108937	GPL24659	PMID_33149261	WT-high-ph rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	data_processing	Supplementary_files_format_and_content: tab-delimited text files containing FPKM values for each sample PGCGROWTHCONDITIONS
SRR7057988	GSE111094	GSM3108937	GPL24659	PMID_33149261	WT-high-ph rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	extract_protocol	Three milliliters of cells from mid-log phase culture were mixed with 6 ml RNAprotect Bacteria Reagent (Qiagen), mixed immediately by vortexing for 5 seconds, incubated for 5 minutes at room temperature, and then centrifuged at 5000g for 10 minutes. The supernatant was decanted and any residual supernatant was removed, then samples were frozen at -80℃. Next, RNA was harvested using RNeasy Plus Mini kit (Qiagen) in accordance with the manufacturer’s instruction. Illumina Ribo-Zero rRNA removal kit (bacteria) (MRZMB126) was used with 1 ug of total RNA for the removal of rRNA procedure. Then KAPA RNA HyperPrep kits(Cat.No.08098107702) was used with rRNA-depleted RNA samples for the construction of sequencing libraries. PGCGROWTHCONDITIONS
SRR7057988	GSE111094	GSM3108937	GPL24659	PMID_33149261	WT-high-ph rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	extract_protocol	RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
SRR7057988	GSE111094	GSM3108937	GPL24659	PMID_33149261	WT-high-ph rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	glycerol stocks of E. coli strains were inoculated into M9 minimal media with the glucose M9 minimal medium for each TF candidate. The concentration of carbon sources was 0.2% (w/v). M9 minimal media was also supplemented with 1 ml trace element solution (100X). 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) PGCGROWTHCONDITIONS
SRR7057988	GSE111094	GSM3108937	GPL24659	PMID_33149261	WT-high-ph rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	organism	Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
SRR7057988	GSE111094	GSM3108937	GPL24659	PMID_33149261	WT-high-ph rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	source_name	bacteria cells PGCGROWTHCONDITIONS
SRR7057988	GSE111094	GSM3108937	GPL24659	PMID_33149261	WT-high-ph rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR7057988	GSE111094	GSM3108937	GPL24659	PMID_33149261	WT-high-ph rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	medium: glucose M9 minimal pH8.5 PGCGROWTHCONDITIONS
SRR7057988	GSE111094	GSM3108937	GPL24659	PMID_33149261	WT-high-ph rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS
SRR7057988	GSE111094	GSM3108937	GPL24659	PMID_33149261	WT-high-ph rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: wild type PGCGROWTHCONDITIONS
SRR7057988	GSE111094	GSM3108937	GPL24659	PMID_33149261	WT-high-ph rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	glycerol stocks of E. coli strains were inoculated into M9 minimal media with the glucose M9 minimal medium for each TF candidate. The concentration of carbon sources was 0.2% (w/v). M9 minimal media was also supplemented with 1 ml trace element solution (100X). 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) PGCGROWTHCONDITIONS
SRR7057988	GSE111094	GSM3108937	GPL24659	PMID_33149261	WT-high-ph rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	organism	Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
SRR7057988	GSE111094	GSM3108937	GPL24659	PMID_33149261	WT-high-ph rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	source_name	bacteria cells PGCGROWTHCONDITIONS
SRR7057988	GSE111094	GSM3108937	GPL24659	PMID_33149261	WT-high-ph rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	contact_name	Donghyuk,,Kim PGCGROWTHCONDITIONS