Microbiota-driven epigenetic alterations in intestinal epithelial cells [ChIP-seq]

We compare H3K9Ac enrichment in intestinal epithelial cells from intestine of germ-free and microbiota-replete (conventionally-housed) mice. Intestinal epithelial cells were harvested from the intestine of conventional or germ-free C57Bl6J mice. Chromatin immunoprecipitation was performed with anti-H3K9Ac. Sequencing was performed using the Illumina HiSeq2500. Reads were mapped to the mm10 genome using Bowtie. Microbiota induce loss of H3K9Ac within mulitple sites of the Clec2e gene. Overall design: Intestinal epithelial cells were harvested from the intestine of conventional or germ-free C57Bl6J mice, and ChIPseq was performed using H3K9Ac.