"Illumina Casava1.7 software used for basecalling."	"data_processing.1"
"All raw FastQ files generated were filtered using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/)."	"data_processing.2"
"Reads per kilobase of exon model per million mapped reads (RPKM) was used as a normalized metric to present the gene expression levels.(Nature methods 2008, 5: 621-628)"	"data_processing.3"
"Transcripts evaluation of differential expression were accomplished using MARS (MA-plot-based method with Random sampling model) in DEGseq package.(Bioinformatics 2010, 26: 136-138)"	"data_processing.4"
"Genome_build: NC_002655.2"	"data_processing.5"
"Supplementary_files_format_and_content: RPKM"	"data_processing.6"
"RNA extraction was performed using RiboPure-BacteriaTM Bacteria kit according to the manufacturer's protocol (Ambion, Life Technologies). DNase I treatment was applied to eliminate genomic DNA contamination as per the manufacturer's recommendations."	"extract_protocol_ch1.1"
"RNA libraries were prepared for sequencing using standard Illumina protocols"	"extract_protocol_ch1.2"
"Overnight cultures of bacteria were diluted 1:100 in fresh LB broth and grown to logarithmic phase at an OD600 of about 0.8."	"growth_protocol_ch1.1"
"Escherichia coli O157:H7 str. EDL933"	"organism_ch1.1"
"Enterohemorrhagic Escherichia coli O157:H7 strain EDL933"	"source_name_ch1.1"
"wt_1"	"title.1"
"The bacteria were centrifuged at 4000×g at 4°C for 5 min and then washed with PBS."	"treatment_protocol_ch1.1"
"RNA-Seq"	"library_strategy.1"
"genotype: wild type"	"characteristics_ch1.1"
"phase: logarithmic phase"	"characteristics_ch1.2"
"Overnight cultures of bacteria were diluted 1:100 in fresh LB broth and grown to logarithmic phase at an OD600 of about 0.8."	"growth_protocol_ch1.1"
"Escherichia coli O157:H7 str. EDL933"	"organism_ch1.1"
"Enterohemorrhagic Escherichia coli O157:H7 strain EDL933"	"source_name_ch1.1"
"The bacteria were centrifuged at 4000×g at 4°C for 5 min and then washed with PBS."	"treatment_protocol_ch1.1"