SRR9204650	GSE122295	GSM3854835	GPL21433	PMID_31797920	bw_delpurR_cytd__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	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
SRR9204650	GSE122295	GSM3854835	GPL21433	PMID_31797920	bw_delpurR_cytd__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	data_processing	Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode PGCGROWTHCONDITIONS
SRR9204650	GSE122295	GSM3854835	GPL21433	PMID_31797920	bw_delpurR_cytd__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	data_processing	Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size. PGCGROWTHCONDITIONS
SRR9204650	GSE122295	GSM3854835	GPL21433	PMID_31797920	bw_delpurR_cytd__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	data_processing	Genome_build: NC_000913.3 PGCGROWTHCONDITIONS
SRR9204650	GSE122295	GSM3854835	GPL21433	PMID_31797920	bw_delpurR_cytd__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	data_processing	Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample PGCGROWTHCONDITIONS
SRR9204650	GSE122295	GSM3854835	GPL21433	PMID_31797920	bw_delpurR_cytd__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	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
SRR9204650	GSE122295	GSM3854835	GPL21433	PMID_31797920	bw_delpurR_cytd__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
SRR9204650	GSE122295	GSM3854835	GPL21433	PMID_31797920	bw_delpurR_cytd__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	growth_protocol	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
SRR9204650	GSE122295	GSM3854835	GPL21433	PMID_31797920	bw_delpurR_cytd__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR9204650	GSE122295	GSM3854835	GPL21433	PMID_31797920	bw_delpurR_cytd__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	source_name	E. coli BW25113 PGCGROWTHCONDITIONS
SRR9204650	GSE122295	GSM3854835	GPL21433	PMID_31797920	bw_delpurR_cytd__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR9204650	GSE122295	GSM3854835	GPL21433	PMID_31797920	bw_delpurR_cytd__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	strain: BW25113 PGCGROWTHCONDITIONS
SRR9204650	GSE122295	GSM3854835	GPL21433	PMID_31797920	bw_delpurR_cytd__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose and 1 mM cytidine PGCGROWTHCONDITIONS
SRR9204650	GSE122295	GSM3854835	GPL21433	PMID_31797920	bw_delpurR_cytd__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	growth_protocol	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
SRR9204650	GSE122295	GSM3854835	GPL21433	PMID_31797920	bw_delpurR_cytd__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR9204650	GSE122295	GSM3854835	GPL21433	PMID_31797920	bw_delpurR_cytd__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	source_name	E. coli BW25113 PGCGROWTHCONDITIONS
SRR9204650	GSE122295	GSM3854835	GPL21433	PMID_31797920	bw_delpurR_cytd__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	contact_name	Anand,,Sastry PGCGROWTHCONDITIONS