Comparative transcriptomic analysis of Crohn's-associated Escherichia coli in laboratory and host environments

We used next generation sequencing to sequence the transcriptome of AIEC str. NRG857c and identify the genes that are differentially regulated in the gut. RNA was extracted from AIEC populations in vitro and in the ceca of infected hosts. Transcriptomes were sequenced using the Illumina HiSeq 2000 platform and the processed data was used for differential gene expression analysis to map the genes that are differentially regulated in vivo.