Chromatin accessibility in the mouse intestinal epithelium across different regions and life stages

We compare the epigenomes of mouse intestinal epithelial cells at different intestinal regions and life stages of the mouse. We use a sequencing assay for transposase accessible chromatin (ATAC-seq) to determine highly accessible genomic regions. We determine regions that are differentially accessible between intestinal regions (duodenal crypt, duodenal villus, and colon) and between life stages (12-to-15-day-old/juvenile, 90-day-old/adult, and 21-month-old/geriatric). The experiment was designed to compare chromatin accessibility between mice of different ages and within different regions of the intestinal tract. The mouse subjects were divided into three age groups: juvenile mice, which were harvested twelve to fifteen days after birth; adult mice, which were harvested three months after birth; and geriatric mice, which were harvested twenty-one months after birth. Each age group includes three biological replicates (nine mice total). The sequencing data for a proximal colon sample from one geriatric mouse replicate in the colon were discarded due to poor DNA quality. Duodenum epithelial cells and colon epithelial cells were extracted from juvenile mice. Duodenum villus epithelial cells, duodenum crypt epithelial cells, and colon epithelial cells were extracted from adult mice. Duodenum villus epithelial cells, duodenum crypt epithelial cells, and proximal colon epithelial cells were extracted from geriatric mice. Each age and tissue combination formed a condition (8 conditions total).