Differential RNA-Seq (dRNA-seq) of Escherichia coli O104:H4

We performed a high-throughput mapping of the 5’ end transcriptome of the pAA plasmid of the clinical Escherichia coli O104:H4 (E. coli O104:H4) isolate LB226692. We employed differential RNA-sequencing (dRNA-seq), a terminator exonuclease (TEX)-based RNA-seq approach allowing for the discrimination of primary and processed transcripts. This method has proven to be a powerful tool for the mapping of transcription start sites (TSS) and detection of non-coding RNAs (ncRNAs) in bacteria. We catalogued pAA-associated TSS and processing sites on a plasmid-wide scale and performed a detailed analysis of the primary transcriptome focusing on pAA virulence gene expression. Overall design: Exponentially growing E. coli O104:H4 isolate LB226692 was subjected to dRNA-seq. A detailed analysis of the pAA plasmid primary transcriptome focusing on virulence gene expression was performed