RNA sequencing based analysis of the bacterial transcriptome

To investigate the architecture of the E. coli K-12 transcriptome, we used two RNA-Seq technologies to analyze strand-specific transcription at single-nucleotide resolution. We analyzed the data by using an organizational schema to annotate the promoters and terminators that define transcription units across the genome. We found substantial evidence for differential gene expression within complex operons, which we categorized based on operon architecture. E. coli K-12 strain MG1655 substrain BW38028 and isogenic rpoS mutant were cultured in minimal glucose media (carbon, nitrogen, or phosphate limited) and the total transcriptome of log and stationary phase samples was sequenced.