SRR8164477	GSE122211	GSM3461157	GPL17024-GPL17439-GPL18995-GPL25769	PMID_31797920	MG_no_te_2	Expression profiling of E. coli K-12 MG1655	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	data_processing	Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2 PGCGROWTHCONDITIONS
SRR8164477	GSE122211	GSM3461157	GPL17024-GPL17439-GPL18995-GPL25769	PMID_31797920	MG_no_te_2	Expression profiling of E. coli K-12 MG1655	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	data_processing	Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
SRR8164477	GSE122211	GSM3461157	GPL17024-GPL17439-GPL18995-GPL25769	PMID_31797920	MG_no_te_2	Expression profiling of E. coli K-12 MG1655	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	data_processing	Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
SRR8164477	GSE122211	GSM3461157	GPL17024-GPL17439-GPL18995-GPL25769	PMID_31797920	MG_no_te_2	Expression profiling of E. coli K-12 MG1655	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	data_processing	Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
SRR8164477	GSE122211	GSM3461157	GPL17024-GPL17439-GPL18995-GPL25769	PMID_31797920	MG_no_te_2	Expression profiling of E. coli K-12 MG1655	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	data_processing	Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
SRR8164477	GSE122211	GSM3461157	GPL17024-GPL17439-GPL18995-GPL25769	PMID_31797920	MG_no_te_2	Expression profiling of E. coli K-12 MG1655	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	extract_protocol	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
SRR8164477	GSE122211	GSM3461157	GPL17024-GPL17439-GPL18995-GPL25769	PMID_31797920	MG_no_te_2	Expression profiling of E. coli K-12 MG1655	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	extract_protocol	RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
SRR8164477	GSE122211	GSM3461157	GPL17024-GPL17439-GPL18995-GPL25769	PMID_31797920	MG_no_te_2	Expression profiling of E. coli K-12 MG1655	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	growth_protocol	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
SRR8164477	GSE122211	GSM3461157	GPL17024-GPL17439-GPL18995-GPL25769	PMID_31797920	MG_no_te_2	Expression profiling of E. coli K-12 MG1655	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	organism	Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
SRR8164477	GSE122211	GSM3461157	GPL17024-GPL17439-GPL18995-GPL25769	PMID_31797920	MG_no_te_2	Expression profiling of E. coli K-12 MG1655	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	source_name	E. coli K12 MG1655 PGCGROWTHCONDITIONS
SRR8164477	GSE122211	GSM3461157	GPL17024-GPL17439-GPL18995-GPL25769	PMID_31797920	MG_no_te_2	Expression profiling of E. coli K-12 MG1655	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR8164477	GSE122211	GSM3461157	GPL17024-GPL17439-GPL18995-GPL25769	PMID_31797920	MG_no_te_2	Expression profiling of E. coli K-12 MG1655	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	characteristics	strain: MG1655 PGCGROWTHCONDITIONS
SRR8164477	GSE122211	GSM3461157	GPL17024-GPL17439-GPL18995-GPL25769	PMID_31797920	MG_no_te_2	Expression profiling of E. coli K-12 MG1655	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	characteristics	media: M9 minimal media w/ 0.2% glucose w/o trace elements PGCGROWTHCONDITIONS
SRR8164477	GSE122211	GSM3461157	GPL17024-GPL17439-GPL18995-GPL25769	PMID_31797920	MG_no_te_2	Expression profiling of E. coli K-12 MG1655	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	characteristics	knock-out: -- PGCGROWTHCONDITIONS
SRR8164477	GSE122211	GSM3461157	GPL17024-GPL17439-GPL18995-GPL25769	PMID_31797920	MG_no_te_2	Expression profiling of E. coli K-12 MG1655	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	growth_protocol	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
SRR8164477	GSE122211	GSM3461157	GPL17024-GPL17439-GPL18995-GPL25769	PMID_31797920	MG_no_te_2	Expression profiling of E. coli K-12 MG1655	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	organism	Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS
SRR8164477	GSE122211	GSM3461157	GPL17024-GPL17439-GPL18995-GPL25769	PMID_31797920	MG_no_te_2	Expression profiling of E. coli K-12 MG1655	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	source_name	E. coli K12 MG1655 PGCGROWTHCONDITIONS
SRR8164477	GSE122211	GSM3461157	GPL17024-GPL17439-GPL18995-GPL25769	PMID_31797920	MG_no_te_2	Expression profiling of E. coli K-12 MG1655	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	contact_name	Anand,,Sastry PGCGROWTHCONDITIONS