Global gene expression of EHEC O26:H11 21765 and O157:H7 EDL933 strains in ground beef with or without microflora

The genomic expression profiles of enterohemorrhagic Escherichia coli O26:H11 21765 and O157:H7 EDL933 strains grown in ground beef enriched in microflora were compared with the corresponding expression profiles in ground beef without microflora. For our application of RNA-Seq, 3 biological replicates were performed. To reduce the possibility of spurious alignment and crosstalk between the reference genome of EHEC and other similar genomes, the transcriptionally up-regulated genes in presence of microflora were filtered for E. coli specific genes. This constraint also influenced our sequencing strategy, sequencing mode (paired-end sequencing), library-type (strand-specific cDNA library) and choice of the read length (125 bp). The paired-end strand-specific RNA-Seq with a read length of 125 bp informations allow for higher levels of specific alignments, thus reduce the possibility of spurious alignment between the reference genome and other similar genomes.