"Illumina Casava1.7 software used for basecalling."	"data_processing.1"
"Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to E.coli K2 BW25113 whole genome using bowtie v0.12.2"	"data_processing.2"
"Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009."	"data_processing.3"
"Genome_build: E.coli K12 BW25113"	"data_processing.4"
"Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample."	"data_processing.5"
"After chilling on ice, each 100-ml culture was mixed with 25 ml ice-cold ethanol/phenol solution (5% (v/v), water-saturated phenol in 95% (v/v) ethanol).  Cells were harvested by centrifugation at 7,000 g for 2 min at 4 °C, flash-frozen with dry ice, and stored at –80 °C. Two independent cultures for each sample were mixed together for determination of transcriptional profiles. Total RNA was extracted from the collected bacterial cells using TRIzol reagent (Thermo Fisher Scientifc)."	"extract_protocol_ch1.1"
"rRNA was removed from total RNA by using the Ribo-Zero rRNA removal kit. Reverse transcription and cDNA amplification were performed with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech). Libraries were constructed using the Illumina Nextera XT kit and analyzed for concentration , size distribution and quantification of viable sequencing templates via qPCR."	"extract_protocol_ch1.2"
"To generate Illumina-compatible sequencing libraries for each sample, molecular indexes were added to each library, allowing samples to be pooled and sequenced on the Illumina HiSeq 2500 with a 1 x 50 bp single-end configuration. More than 250 million reads were generated per sample, and at least 80% bases had quality scores above Q30."	"extract_protocol_ch1.3"
"Overnight cultures of the dnaB-Ts single mutant (strain 2429) and the dnaB-Ts ΔahpC double mutant (strain 3780) were diluted 100-fold into fresh SB medium (3.2% peptone, 2% yeast extract and 1% NaCl), and they were then grown at 30 °C to early-log phase (OD600 = 0.15).  Next these log-phase cultures were diluted 20-fold into 200 ml pre-warmed, fresh SB medium, and they were grown at 30 °C for another 60 min."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Bacterial cultures"	"source_name_ch1.1"
"dnaB-Ts ΔahpC_42°C"	"title.1"
"Samples (200-ml) of the above cultures for each strain were split into two aliquots (each 100 ml), and the aliquots were then incubated at 30 °C or 42 °C for another 60 min."	"treatment_protocol_ch1.1"
"RNA-Seq"	"library_strategy.1"
"strain: 3780"	"characteristics_ch1.1"
"culture temperature: 42 °C for 60 min"	"characteristics_ch1.2"
"medium: SB broth"	"characteristics_ch1.3"
"Overnight cultures of the dnaB-Ts single mutant (strain 2429) and the dnaB-Ts ΔahpC double mutant (strain 3780) were diluted 100-fold into fresh SB medium (3.2% peptone, 2% yeast extract and 1% NaCl), and they were then grown at 30 °C to early-log phase (OD600 = 0.15).  Next these log-phase cultures were diluted 20-fold into 200 ml pre-warmed, fresh SB medium, and they were grown at 30 °C for another 60 min."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Bacterial cultures"	"source_name_ch1.1"
"Samples (200-ml) of the above cultures for each strain were split into two aliquots (each 100 ml), and the aliquots were then incubated at 30 °C or 42 °C for another 60 min."	"treatment_protocol_ch1.1"