<i>Escherichia coli</i> transcriptome assembly from a compendium of RNA-seq data sets

Owing to the complexities of bacterial RNA biology, the transcriptomes of even the best studied bacteria are not fully understood. To help elucidate the transcriptional landscape of <i>E. coli</i>, we compiled a compendium of 3,376 RNA-seq data sets composed of more than 7 trillion sequenced bases, which we evaluate with a transcript assembly pipeline. We report expression profiles for all annotated <i>E. coli</i> genes as well as 5,071 other transcripts. Additionally, we observe hundreds of instances of co-transcribed genes that are novel with respect to existing operon databases. By integrating data from a large number of sequencing experiments corresponding to a wide range of conditions, we are able to obtain a comprehensive view of the <i>E. coli</i> transcriptome.