RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens

Here, we investigated the impact of Stx2 phage carriage on Escherichia coli (E. coli) K-12 MG1655 host gene expression. Using quantitative RNA-seq analysis, we compared the transcriptome of naïve MG1655 and the lysogens carrying the Stx2 phage of the 2011 E. coli O104:H4 outbreak strain or of the E. coli O157:H7 strain PA8, which share high degree of sequence similarity. Exponentially growing E. coli K-12 MG1655, MG1655::φO104 (carrying the Stx2 phage of E. coli O104:H4) and MG1655::φPA8 (carrying the Stx2 phage of E. coli O157:H7 PA8) cells were subjected to strand specific RNA-seq. Three biological replicates per strain were included. DESeq2 analysis based on the reads mapped to the E. coli MG1655 genome was performed to identify examples of differential gene expression in the Stx2 lysogens in comparison to naive E. coli MG1655.