"strain: CFT073"	"characteristics_ch1.1"
"plasmid: pBAD-tosR"	"characteristics_ch1.2"
"qC: We checked the quality of the raw reads data for each sample using FastQC (version 0.11.3) to identify features of the data that may indicate quality problems (e.g. low quality scores, over-represented sequences, inappropriate GC content, etc.)."	"data_processing.1"
"Alignment, Quantiatino and Normalization, Differential Expression : We used the SPARTA(version 1) software package for alignment, differential expression analysis, and post-analysis diagnostics. SPARTA is an RNA-Seq package specifically designed for bacterial studies. It uses the Bowtie(version 1.1.1) short read aligner, HTSeq(version 0.6.1) to count gene features, and edgeR for differential expression."	"data_processing.2"
"Annotation : The reference genome (Escherichia_coli_cft073.ASM744v1.dna.chromosome.Chromosome.fa) and annotations (Escherichia_coli_cft073.ASM744v1.32.gtf ) were downloaded from EnsemblBacteria"	"data_processing.3"
"Genome_build: CFT073 E. coli"	"data_processing.4"
"Supplementary_files_format_and_content: .xls,  spreadsheet of normalized read counts for each gene for each sample, differential expression data, and annotation"	"data_processing.5"
"Cells were then lysed with 0.2 µM of lysozyme in TE (10 mM Tris-Cl, 1 mM EDTA, pH 8.0) for 5 min at room temperature, and total RNA was extracted using the RNeasy Mini Kit (Qiagen). DNA contamination was eliminated by treatment with TURBO DNase (Thermo Fisher). Depletion of ribosomal RNA was accomplished with the Ribominus Transcriptome Isolation Kit (Thermo Fisher) followed by ethanol precipitation."	"extract_protocol_ch1.1"
"Depletion of ribosomal RNA was accomplished with the Ribominus Transcriptome Isolation Kit (Thermo Fisher) followed by ethanol precipitation. A stranded library was prepared using a ScriptSeq kit (Illumina) using manufacturer’s recommended protocols.  Each sample was tagged with a six nucleotide barcode unique to each sample to allow multiplexing. The products are purified and enriched by PCR to create the final cDNA library. Final libraries were checked for quality and quantity by TapeStation (Agilent) and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (Kapa Biosystems) following the manufacturer's recommended protocols.  Six samples were sequenced per lane on a 50 cycle single end run on a HiSeq 2500 (Illumina) in high output mode using version 4 reagents."	"extract_protocol_ch1.2"
"E. coli CFT073 carrying either pBAD or pBAD-tosR-his6 were cultured overnight in biological triplicates in LB medium containing ampicillin (100 µg/ml). Cultures were diluted 1:100 into fresh LB medium containing 10 mM L-arabinose and ampicillin and cultured at 37°C with aeration. A 400 µL sample was collected between OD600 0.46-0.96, and stabilized by the immediate addition of 800 µl of RNAprotect (Qiagen)."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Bacteria"	"source_name_ch1.1"
"CFT073 +pBAD-tosR rep 3"	"title.1"
"RNA-Seq"	"library_strategy.1"
"strain: CFT073"	"characteristics_ch1.1"
"plasmid: pBAD-tosR"	"characteristics_ch1.2"
"E. coli CFT073 carrying either pBAD or pBAD-tosR-his6 were cultured overnight in biological triplicates in LB medium containing ampicillin (100 µg/ml). Cultures were diluted 1:100 into fresh LB medium containing 10 mM L-arabinose and ampicillin and cultured at 37°C with aeration. A 400 µL sample was collected between OD600 0.46-0.96, and stabilized by the immediate addition of 800 µl of RNAprotect (Qiagen)."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Bacteria"	"source_name_ch1.1"