Fresh intestinal crypt epithelial cells were collected by removing villi manually and incubating crypts in 5 mM EDTA for 50 min at 4°C. Lgr5+ intestinal stem cells were purified from Lgr5-eGFP-Cre mice using flow cytometry for GFP. Crypt secretory progenitors were enriched by treating mice with the Notch inhibitor Dibenzazepine and enterocyte progenitors were isolated from Atoh1-/- mice, which lack all secretory cells. Cells were fixed in 1% formaldehyde for 25 min at room temperature and lysed. Chromatin was sheared by sonication. DNA was amplified using ThruPLEX-FD kit (Rubicon Genomics).