SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	data_processing	The data output from the Illumina Hiseq System was obtained directly from Vertis PGCGROWTHCONDITIONS
SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	data_processing	For alignment of the reads contained within the fastq files to the E. coli MG1655 reference genome (RefSeq NC_U00096.3), the short read alignment tool Bowtie2 was utilized under default settings.  Bowtie parameters were set to include only perfect matches and map once reads that map to more than one genome location, i.e., uniquely mapped reads are retained. The output Bowtie2 was a SAM files for each sample. PGCGROWTHCONDITIONS
SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	data_processing	Used SAMTOOLS (Li, et al., PMID 1950593) to sort and index the SAM files obtained from Bowtie2 and convert them to BAM format. PGCGROWTHCONDITIONS
SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	data_processing	Sequence data was processed by conversion of the sample alignment (BAM) files to strand-specific base count (BigWIG) files. To accomplish this an in-house script was created to extract strand-specific base count data from BAM files (outputs are positive and negative strand BigWIG files). PGCGROWTHCONDITIONS
SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	data_processing	BigWIG files were viewed and annotated using Jbrowse and Integrated Genome Viewer. PGCGROWTHCONDITIONS
SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	data_processing	Genome_build: Reference genome for E. coli MG1655 (RefSeq NC_000913.3). PGCGROWTHCONDITIONS
SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	data_processing	Supplementary_files_format_and_content: BigWIG files are provided showing uniquely mapped sequence reads. PGCGROWTHCONDITIONS
SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	extract_protocol	All samples were extracted using the hot phenol extraction with DNA digestion, following standard protocol PGCGROWTHCONDITIONS
SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	extract_protocol	cDNA libraries were constructed at Vertis in Germany using a ligation based stratagey for Illumina whole transcriptome sequencing. Total RNA (DNase I digested) was fragmented by RNase III. RNA samples labeled as TEX were also subsequently digested with Terminator Exonuclease (TEX). Pyrophosphate groups were removed from the 5′ terminus using tobacco acid pyrophosphatase (TAP), and an RNA adapter was ligated to the 5′ end of the RNA. First-strand synthesis was performed using standard Illumina protocols. PGCGROWTHCONDITIONS
SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	growth_protocol	Wild type E. coli K-12 (strain BW38038) and BW39452(ΔrpoS) cultures were grown on MOPS glucose minimal medium with 0.2% glucose as sole carbon source at 37°C, pH was initially 7.4,  and the agitation speed was 500 rpm. Culture samples were harvested during logarithmic growth and  following entry into stationary phase for the WT and rpoS mutant. OD600 measurements were made on a Beckman Coulter DU 800 spectrophotometer. Samples were harvested directly into ice-cold RNAlater at a 1:1 dilution to protect RNA from degradation and cells then were pelleted by centrifugation at 8000rpm for 10 minutes. Cell pellets were stored at -80°C in an equal volume of RNAlater prior to RNA extraction. PGCGROWTHCONDITIONS
SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	organism	Escherichia coli BW38028 PGCGROWTHCONDITIONS
SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	source_name	Cell culture PGCGROWTHCONDITIONS
SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	treatment_protocol	Prior to total RNA extraction harvested bacterial cells were stored at -80.0°C in an equal volume of RNAlater. PGCGROWTHCONDITIONS
SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	characteristics	strain: BW38028 PGCGROWTHCONDITIONS
SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	characteristics	genotype: wt PGCGROWTHCONDITIONS
SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	characteristics	treatment: log phase sample PGCGROWTHCONDITIONS
SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	characteristics	growth phase: Log phase OD 0.4 PGCGROWTHCONDITIONS
SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	characteristics	sample type: no RNA treatment PGCGROWTHCONDITIONS
SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	growth_protocol	Wild type E. coli K-12 (strain BW38038) and BW39452(ΔrpoS) cultures were grown on MOPS glucose minimal medium with 0.2% glucose as sole carbon source at 37°C, pH was initially 7.4,  and the agitation speed was 500 rpm. Culture samples were harvested during logarithmic growth and  following entry into stationary phase for the WT and rpoS mutant. OD600 measurements were made on a Beckman Coulter DU 800 spectrophotometer. Samples were harvested directly into ice-cold RNAlater at a 1:1 dilution to protect RNA from degradation and cells then were pelleted by centrifugation at 8000rpm for 10 minutes. Cell pellets were stored at -80°C in an equal volume of RNAlater prior to RNA extraction. PGCGROWTHCONDITIONS
SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	organism	Escherichia coli BW38028 PGCGROWTHCONDITIONS
SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	source_name	Cell culture PGCGROWTHCONDITIONS
SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	treatment_protocol	Prior to total RNA extraction harvested bacterial cells were stored at -80.0°C in an equal volume of RNAlater. PGCGROWTHCONDITIONS
SRR1411272	GSE58556	GSM1413874	GPL18814	PMID_25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	contact_name	James,,Creecy PGCGROWTHCONDITIONS