"We used an Illumina NextSeq 500 system and a MID 150 Kit with 1x75 bp read length. Base-calling was perform online during the sequencing procedure with the Real-Time Analysis (RTA) software version 2.4.11 and System Suite Version 2.1.2.1."	"data_processing.1"
"Illumina sequencing instruments generate per-cycle BCL base call files as primary sequencing output in bcl2 format. Conversion of the bcl2 file to gzipped fastq files was performed using the bcl2fastq script v. 2.18.0.12 provided by Illumina."	"data_processing.2"
"Quality and adapter trimming was performed with the CLC Genomics Workbench 9.0 software package using the 'Trim Sequences' tool with standard parameters."	"data_processing.3"
"Mapping of the trimmed reads to the reference sequences was also performed with the CLC Genomics Workbench 9.0 using the 'Map Reads to Reference' tool with standard parameters."	"data_processing.4"
"For quantification of gene expression (read counting), the alignments generated with the Genomics Workbench were exported in BAM format. Read counting was then performed with the FeatureCounts v. 1.5.0-p1 program using the following parameters; Level : meta-feature leve. Paired-end : no. Strand specific : yes. Multimapping reads : counted (as fractions). Multi-overlapping reads : not counted. Overlapping bases : 30. Read orientations : fr"	"data_processing.5"
"Genome_build: NCBI reference sequence (NC_017626.1)"	"data_processing.6"
"Supplementary_files_format_and_content: Strain-expression.xlsx archive contains expression values in RPKM (Reads Per Kb exon (contig) per Million mapped  reads ( see Mortazavi et al. 2008, Nat Methods. 5(7):621-8 ) and can be directly compared to each other)  tab-delimited text files include RPKM values for each Sample."	"data_processing.7"
"Total RNA was isolated from the cell pellets using a bead mill and the mirVana RNA isolation kit (Ambion) including DNase treatment. From the total RNA samples, ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Removal Kit for bacteria (Illumina)."	"extract_protocol_ch1.1"
"From the rRNA depleted RNA samples, first-strand cDNA was synthesized using a N6 randomized primer. After fragmentation, the Illumina TruSeq sequencing adapters were ligated in a strand specific manner to the 5' and 3' ends of the cDNA fragments. The cDNA was finally amplified with PCR (15 PCR cycles) using a proof reading enzyme. For Illumina sequencing, cDNA libraries were pooled in a 25:1 ratio. The library pool was fractionated in the size range of 250-500 bp using a differential clean- up with the Agencourt AMPure kit. The cDNA pool was sequenced on an Illumina NextSeq 500 system using 75 bp read length."	"extract_protocol_ch1.2"
"LB medium at 37ºC with 200rpm agitation."	"growth_protocol_ch1.1"
"Escherichia coli 042"	"organism_ch1.1"
"cell pellets"	"source_name_ch1.1"
"E. coli 042 WT"	"title.1"
"RNA-Seq"	"library_strategy.1"
"genotype: wild type"	"characteristics_ch1.1"
"LB medium at 37ºC with 200rpm agitation."	"growth_protocol_ch1.1"
"Escherichia coli 042"	"organism_ch1.1"
"cell pellets"	"source_name_ch1.1"