Comparative transcriptome analysis of a panel of Escherichia coli natural isolates

The link between phylogeny, gene expression and adaptation remains vague in bacteria. Here we compare the transcriptome of 16 E. coli stains isolated from various sources and spanning most common E. coli phylogroups (A, B1, B2, D, E and, F) and lifestyles. Total RNAs were extracted after growth of three biological replicates in lysogeny broth medium to exponential phase. After quality control on an Agilent 2100 Bioanalyzer. Samples were prepared for sequencing using the TruSeq® Stranded Total RNA Kit (Illumina) and sequenced on a NextSeq 500 benchtop sequencer (Illumina).