Escherichia coli O157:H7  Transcriptome
Bacteria were incubated in RNA  stabilization reagent (Qiagen) for 2 min and then centrifuged at 8000 g for 2  min and resuspended in RNA stabilization reagent. The cells were lysed by  TRIzol and rRNA was removed via mRNA-only prokaryotic mRNA isolation kit  (Epicentre Biotech, Madison, WI, USA). Sequencing was performed by using  Illumina HiSeqTM 2000 with paired-end 100 bp reads (Illumina, San Diego, CA,  USA). Qualified reads were mapped to the genome of E. coli O157:H7 via SOAP2.  Gene expression levels were expressed as RPKM (mapped reads per kilobase per  million reads).