"Vertis Biotechnologie AG bioinformatics department did a preliminary analysis of the high-throughput sequencing results which included the mapping of the reads against E. coli genome (NC_000913 downloaded from NCBI genome database)."	"data_processing.1"
"We then used the mapped files to run Cufflinks (estimates the relative abundance of the transcripts) and after Cuffdiff to find significant changes in transcript expression when comparing two samples (Trapnell, Williams et al. 2010)."	"data_processing.2"
"Genome_build: ASM584v2"	"data_processing.3"
"Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …"	"data_processing.4"
"RNA was isolated following cell lysis and phenol:chloroform extraction as previously described (Andrade, Pobre et al. 2012). After precipitation step in ethanol and 300 mM sodium acetate, RNA was resuspended in MilliQ-water. The integrity of RNA samples was evaluated by agarose gel electrophoresis. Turbo DNase (Ambion) treatment was used to remove contaminant DNA."	"extract_protocol_ch1.1"
"RNA libraries were prepared for sequencing by the company Vertis Biotechnologie AG in Germany"	"extract_protocol_ch1.2"
"Overnight cultures from isolated colonies were diluted in fresh medium to an initial OD600~0.03 and grown to exponential phase (OD600~0.3) at 37ºC, with shaking at 200 rpm in Luria-Bertani (LB) medium supplemented with thymine (50 mg ml-1). When required, antibiotics were present at the following concentrations: kanamycin, 50 mg ml-1; tetracycline, 20 mg ml-1; streptomycin/spectinomycin 20 µg ml-1."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Culture cells"	"source_name_ch1.1"
"WT_RNA-Seq"	"title.1"
"RNA-Seq"	"library_strategy.1"
"strain: K12-MG1693"	"characteristics_ch1.1"
"growth phase: Exponential Phase"	"characteristics_ch1.2"
"genotype: Wild-type"	"characteristics_ch1.3"
"Overnight cultures from isolated colonies were diluted in fresh medium to an initial OD600~0.03 and grown to exponential phase (OD600~0.3) at 37ºC, with shaking at 200 rpm in Luria-Bertani (LB) medium supplemented with thymine (50 mg ml-1). When required, antibiotics were present at the following concentrations: kanamycin, 50 mg ml-1; tetracycline, 20 mg ml-1; streptomycin/spectinomycin 20 µg ml-1."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Culture cells"	"source_name_ch1.1"