Transcriptomic analysis of E. coli Nissle in a DSS-mouse model of colitis

We report a comparative transcriptomic profile of Escherichia coli Nissle 1917 within the context of a mono-colonized DSS-mouse model of colitis to determine the effect of inflammation on the probiotic and find transcriptional biomarkers for IBD. Brief experimental protocol: Germ-free mice were mono-colonized with chloramphenicol resistant E.coli Nissle by oral gavage. The mice were divided into two treatment groups: 1) control mice (mouse ID: DC4,DC5, DC6,DC7); 2) DSS-treated mice (mouse ID: DC1, DC2, DC3, DC8, DC9). DSS-treated mice were given 2% DSS water for 5 days whereas control mice were kept on normal water. Distal colon stool samples were dissected from all mice two days after the end of the DSS treatment at the peak of inflammation. RNA was extracted from stool samples and prepared for RNA-seq. Sequencing libraries were processed using Illumina HiSeq2500 platform, 1 lane, 125bp paired reads. There are two sequencing data file for paired reads of each samples (labelled DC#_R1 and DC#_R2).