"strain: JPEP22"	"characteristics_ch1.1"
"genotype/variation: {delta}perC::kanR, coisogenic to WT"	"characteristics_ch1.2"
"source: Bustamante et al., 2011"	"characteristics_ch1.3"
"For the whole-transcriptome analysis, sequencing was verified using FASTQC (version 0.11.2) to confirm base-call quality in each indexed file."	"data_processing.1"
"Indices corresponding to the same sample were merged, and then uploaded to a cloud-based variant of Galaxy named RNA23 Rocket"	"data_processing.2"
"Using Bowtie2 (version 2.0.2), sequenced reads were mapped to an EPEC O127:H6 reference genome (EMBL/GenBank accession codes FM180568, FM180569, and FM180570)."	"data_processing.3"
"Mapped reads were quality checked with SAMstat (version 1.08), and transcripts were assembled in Cufflinks (version 2.0.2)"	"data_processing.4"
"Differential gene expression (DGE) was then performed on fragments per kilobase mapped (FPKM) values in Cufflinks’ Cuffdiff package (version 0.0.7)."	"data_processing.5"
"DGE analysis used a false-discovery rate (FDR) of 0.10."	"data_processing.6"
"Subsequent data visualizations were performed in R (version 3.1.2) using the cummeRbund package (version 3.0)"	"data_processing.7"
"Genome_build: FM180568"	"data_processing.8"
"Genome_build: FM180569"	"data_processing.9"
"Genome_build: FM180570"	"data_processing.10"
"Supplementary_files_format_and_content: bedgraph: Data presented in a 4 column BED format, of which the first column is the chromosome, the second column is the start position of the chromosome, the third column is the end position, and the fourth column is the fragments per kilobase mapped (FPKM) for that sample. Chromosome positions are specified as 0-relative. The first chromosome position is 0. The last position in a chromosome of length N would be N - 1. Only positions specified have data. Positions not specified do not have data and will not be graphed. All positions specified in the input data are in numerical order."	"data_processing.11"
"Supplementary_files_format_and_content: tabular: Tabular data that informs the excel spreadsheet. The data are averaged across the three samples per strain. Both averaged strain data are presented for each gene on the same line. Data contain gene ID, gene number, locus, fragments per kilobase mapped (FPKM) for WT and mutant strains, log2(fold-change) relative epxression of WT over mutant strains, test-statistic, p-value, q-value, and significance analyzed via the cummeRbund package in R whereby a q-value of <0.05 is considered significant."	"data_processing.12"
"Supplementary_files_format_and_content: xls: The data are averaged across the three samples per strain. Both averaged strain data are presented for each gene on the same line. Excel spreadsheet containing gene ID, gene number, locus, fragments per kilobase mapped (FPKM) for WT and mutant strains, log2(fold-change) relative epxression of WT over mutant strains, test-statistic, p-value, q-value, and significance analyzed via the cummeRbund package in R whereby a q-value of <0.05 is considered significant."	"data_processing.13"
"Samples were diluted 1:1 in RNA Protect (Qiagen, Carlsbad, CA) to inhibit RNase activity and then centrifuged (5000 x g, 10 min). Pellets were resuspended in TE/lysozyme (10 mg/ml lysozyme, 0.5% SDS, pH 8.0) with added proteinase K (1.5 mg/ml). RNA was isolated using Qiagen’s RNeasy kit according to manufacturer instructions with slight modification. Before centrifugation, β-mercaptoethanol was added to RNeasy kit buffer RLT (10% v/v). Additionally, during the wash step RNase-free DNase (Qiagen, Carlsbad, CA) was diluted in RNeasy kit buffer RDD (310 Kunitz units/mL), added to the purification column, and incubated for 15 minutes at room temperature (RT). After isolation, spectrophotometric NanoDrop (NanoDrop 1000 v3.8.1; Thermo Fisher) curves were obtained for each total RNA sample and verified for purity, as defined by absorbance ratios at 260/280 nm and 260/230 nm. Total RNA samples were sent to Oregon State University’s Center for Genome Research and Biocomputing. RNA integrity (RIN) measurements were taken using an Agilent Bioanalyzer, resulting in RIN scores of 10, out of a possible 10, for each sample. Ribosomal RNA was depleted using the RiboZero rRNA removal kit (Life Technologies, Eugene, OR)."	"extract_protocol_ch1.1"
"Resulting mRNA was reverse-transcribed to cDNA libraries via SuperScript III First Strand reverse transcription kit (Invitrogen, Carlsbad, CA, 18080051) as per the manufacturer’s instructions. The cDNA libraries were multiplexed to distinguish replicates from one another, barcoded for sequencing, and then amplified with random hexamers for 15 PCR cycles. Transcripts were sequenced for 50 bases in single-end fashion within one lane of an Illumina Hiseq 2000 flow cell. This yielded roughly 30 million reads per sample."	"extract_protocol_ch1.2"
"LB (5 ml) was inoculated by a frozen stock of WT or perC-mutant strain and incubated at 37°C with 225 rpm shaking. Flasks containing low-glucose DMEM were inoculated 1:100 with the overnight culture and incubated at 37°C with 225 rpm shaking to mid-exponential phase (OD600 0.3-0.5)."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Whole bacterial cell RNA transcriptome"	"source_name_ch1.1"
"ATCACG-D1"	"title.1"
"Incubation and RNA harvesting were carried out for all samples simultaneously and under RNase-free conditions to minimize biological variability in gene expression between each sample. Bacterial concentrations were equalized to the same density (by OD600)."	"treatment_protocol_ch1.1"
"RNA-Seq"	"library_strategy.1"
"strain: JPEP22"	"characteristics_ch1.1"
"genotype/variation: {delta}perC::kanR, coisogenic to WT"	"characteristics_ch1.2"
"source: Bustamante et al., 2011"	"characteristics_ch1.3"
"LB (5 ml) was inoculated by a frozen stock of WT or perC-mutant strain and incubated at 37°C with 225 rpm shaking. Flasks containing low-glucose DMEM were inoculated 1:100 with the overnight culture and incubated at 37°C with 225 rpm shaking to mid-exponential phase (OD600 0.3-0.5)."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Whole bacterial cell RNA transcriptome"	"source_name_ch1.1"
"Incubation and RNA harvesting were carried out for all samples simultaneously and under RNase-free conditions to minimize biological variability in gene expression between each sample. Bacterial concentrations were equalized to the same density (by OD600)."	"treatment_protocol_ch1.1"