"Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings"	"data_processing.1"
"Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count"	"data_processing.2"
"Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor)."	"data_processing.3"
"Lowly expressed genes (<1 read per million) were removed."	"data_processing.4"
"Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor)"	"data_processing.5"
"Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method"	"data_processing.6"
"A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant"	"data_processing.7"
"Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files"	"data_processing.8"
"Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre)."	"extract_protocol_ch1.1"
"Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina)."	"extract_protocol_ch1.2"
"Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"E. coli strain FHI6"	"source_name_ch1.1"
"3.FHI6.nIND.HUS"	"title.1"
"The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C."	"treatment_protocol_ch1.1"
"RNA-Seq"	"library_strategy.1"
"strain: FHI6"	"characteristics_ch1.1"
"group (hus/non-hus): HUS"	"characteristics_ch1.2"
"induced/non-induced: Non-induced"	"characteristics_ch1.3"
"genome accession: GCA_000941895"	"characteristics_ch1.4"
"Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"E. coli strain FHI6"	"source_name_ch1.1"
"The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C."	"treatment_protocol_ch1.1"