"Sequence data from BGI had been filtered to remove reads containing ≥ 10% unreadable bases, ≥ 20% low quality (≤ Q20) bases, adapter contamination or duplicate read-pairs"	"data_processing.1"
"The quality of reads was assessed by using FastQC (Andrews S, 2010) and any reads with a quality score ≤  Q28 were trimmed using Trim Galore! (Krueger F, 2013 )."	"data_processing.2"
"Bowtie 2 (Langmead B & Salzberg SL, 2012) was used with default parameters, to remove any sequence reads aligning to ribosomal RNA, transfer RNA and non-coding RNA sequences."	"data_processing.3"
"RNA-Seq reads were mapped to the reference genome using EDGE-Pro (Magoc T, Wood D and Salzberg SL, 2013) ) with default parameters"	"data_processing.4"
"Differential expression between aerobic and anaerobic environments was identified by using DESeq2 (Love M, Huber W and  Anders S, 2014)"	"data_processing.5"
"Genome_build: Escherichia coli B str. REL606; NC_012967.1"	"data_processing.6"
"Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample"	"data_processing.7"
"RNA was extracted from harvested cultures using a hot lysis buffer and acid phenol-based extraction method and isopropanol precipitation. Following RNA extraction, Turbo DNase (Ambion, USA) was used to treat the samples as per manufacturer’s instructions. Each sample was split into five 20 μL aliquots and two rounds of DNase treatment were performed on each aliquot. Following DNase treatment, RNA samples were purified using the RNeasy Mini kit (Qiagen, Germany) as per the manufacturer’s instructions. For each sample, the DNase-treated aliquots were pooled together before purification. RNA quality was measured using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA) with the RNA 6000 Nano Chip kit according to the manufacturer’s instructions while RNA was quantified using the Quant-iT RNA Assay kit (Life Technologies) and measured on a Qubit® 2.0 fluorometer. RNA was sequenced on the Illumina HiSeq 2000 platform  at BGI (Shenzen, China)."	"extract_protocol_ch1.1"
"RNA libraries were prepared for sequencing using standard Illumina protocols"	"extract_protocol_ch1.2"
"Aerobic and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at 37°C with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture. Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Cultured cells"	"source_name_ch1.1"
"Anaerobic 3"	"title.1"
"RNA-Seq"	"library_strategy.1"
"strain: REL4536"	"characteristics_ch1.1"
"growth phase: Stationary phase"	"characteristics_ch1.2"
"growth environment: Anaerobic"	"characteristics_ch1.3"
"Aerobic and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at 37°C with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture. Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Cultured cells"	"source_name_ch1.1"