"The data output from the Illumina Hiseq System was obtained directly from Vertis"	"data_processing.1"
"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."	"data_processing.2"
"Used SAMTOOLS (Li, et al., PMID 1950593) to sort and index the SAM files obtained from Bowtie2 and convert them to BAM format."	"data_processing.3"
"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)."	"data_processing.4"
"BigWIG files were viewed and annotated using Jbrowse and Integrated Genome Viewer."	"data_processing.5"
"Genome_build: Reference genome for E. coli MG1655 (RefSeq NC_000913.3)."	"data_processing.6"
"Supplementary_files_format_and_content: BigWIG files are provided showing uniquely mapped sequence reads."	"data_processing.7"
"All samples were extracted using the hot phenol extraction with DNA digestion, following standard protocol"	"extract_protocol_ch1.1"
"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."	"extract_protocol_ch1.2"
"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."	"growth_protocol_ch1.1"
"Escherichia coli BW38028"	"organism_ch1.1"
"Cell culture"	"source_name_ch1.1"
"WT_glucose_stat"	"title.1"
"Prior to total RNA extraction harvested bacterial cells were stored at -80.0°C in an equal volume of RNAlater."	"treatment_protocol_ch1.1"
"RNA-Seq"	"library_strategy.1"
"strain: BW38028"	"characteristics_ch1.1"
"genotype: wt"	"characteristics_ch1.2"
"treatment: Carbon starvation"	"characteristics_ch1.3"
"growth phase: 30 min post stationary"	"characteristics_ch1.4"
"sample type: no RNA treatment"	"characteristics_ch1.5"
"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."	"growth_protocol_ch1.1"
"Escherichia coli BW38028"	"organism_ch1.1"
"Cell culture"	"source_name_ch1.1"
"Prior to total RNA extraction harvested bacterial cells were stored at -80.0°C in an equal volume of RNAlater."	"treatment_protocol_ch1.1"