"strain: K-12 MG1655"	"characteristics_ch1.1"
"genotype/variation: delta-gadE"	"characteristics_ch1.2"
"growth phase: mid-log phase (OD600 = 0.3)"	"characteristics_ch1.3"
"Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S"	"data_processing.1"
"Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks v.1.3.0"	"data_processing.2"
"Genome_build: NC_000913"	"data_processing.3"
"Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample."	"data_processing.4"
"Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA)."	"extract_protocol_ch1.1"
"RNA libraries were prepared for sequencing using standard Illumina protocols"	"extract_protocol_ch1.2"
"E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"ΔgadE pH5.5"	"source_name_ch1.1"
"ΔgadE pH5.5 1"	"title.1"
"The cell culture was treated with the RNAprotect reagent (Qiagen)."	"treatment_protocol_ch1.1"
"RNA-Seq"	"library_strategy.1"
"strain: K-12 MG1655"	"characteristics_ch1.1"
"genotype/variation: delta-gadE"	"characteristics_ch1.2"
"growth phase: mid-log phase (OD600 = 0.3)"	"characteristics_ch1.3"
"E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"ΔgadE pH5.5"	"source_name_ch1.1"
"The cell culture was treated with the RNAprotect reagent (Qiagen)."	"treatment_protocol_ch1.1"