Differentiating Mouse Colon and Rectum: Transcriptional Differences and Environmental Exposure

We have demonstrated that the colon and rectum are transcriptionally distinct in mice and that the colon can be differentiated from rectum based on microarray profiles. This transition occurs over the first weeks of life, indicating environmental exposure is an important mediator. Colon and rectum RNA from E18 to 8 week old C57BL/6J mice along with 8 week old gnotobiotic C57BL/6J mice were evaluated with microarray technology. For each array analysis a pool of RNA(2-8) from individual colons or rectums were co-hybridized with a reference pool of 4 RNA samples from mouse small intestine, rectum and colon (SIRC)) to Agilent Mouse Whole Genome 4x44k microarrays and scanned on an Agilent microarray scanner. Files were extracted using Agilent Feature Extraction version 9.5.