"Raw .fastq files were mapped to the reference genome (NC000913.2) using BWA (version 0.7). Mapped reads were then converted to read count per gene using bedtools (version 2).  In the case of Ion torrent data .bam files were converted using BWA."	"data_processing.1"
"Resulting read count matrix was used as input for the differntial expression analysis in edgeR (version 3.12.1)."	"data_processing.2"
"Genome_build: Escherichia coli (NC000913.2)"	"data_processing.3"
"Supplementary_files_format_and_content: .txt (log2 fold change values, p-values)"	"data_processing.4"
"NEXTflexRapid Directional RNA-Seq library kit"	"extract_protocol_ch1.1"
"Cells were inoculated from overnight grown culture in Lysogeny Broth (LB) and then harvested in the early exponential growth phase and mid exponential growth phase."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"cells"	"source_name_ch1.1"
"cya.rep1.me"	"title.1"
"RNA was extracted from the harvested cells using Trizol reagent. Depending upon the concentration of total RNA, sample were treated with Dnase and ribocleanup was given according to the instruction manual."	"treatment_protocol_ch1.1"
"RNA-Seq"	"library_strategy.1"
"srain: K12 MG1671"	"characteristics_ch1.1"
"growth phase: Mid exponential"	"characteristics_ch1.2"
"genotype: cya mutant background"	"characteristics_ch1.3"
"Cells were inoculated from overnight grown culture in Lysogeny Broth (LB) and then harvested in the early exponential growth phase and mid exponential growth phase."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"cells"	"source_name_ch1.1"
"RNA was extracted from the harvested cells using Trizol reagent. Depending upon the concentration of total RNA, sample were treated with Dnase and ribocleanup was given according to the instruction manual."	"treatment_protocol_ch1.1"