SRS9276500 SAMN19844094 10090 Mus musculus Epithelial cells were isolated from the small intestine. In brief, isolated small intestines were opened lengthwise, washed with cold PBS. After removal of villi by scraping with a cold glass slide, samples were chopped into pieces of around 2 mm and further washed with cold PBS. The tissue was then incubated in 2.5 mM EDTA with PBS at 4 degree Celsius for 30 min on a rocking platform at 20 rpm. The supernatant was then removed and the tissue pieces were resuspended in DMEM/F12 (Corning) with 0.1% BSA, shaken vigorously and then filtered through a 70 um strainer (Corning) whilst on ice. Crypts were collected by centrifugation at 4 degree Celsius and then digested with TrypLE Express enzyme 1X (Gibco) and 0.5 mg/ml DNase (Worthington) at 37 degree Celsius for 5 min before filtration through a 40 um strainer (Corning). Single-cell suspensions were prepared as above and resuspended in FACS buffer containing HBSS with 25mM HEPES (Gibco) and 1% fetal bovine serum (Gibco). Antibody staining was performed at 4 degree Celsius for 30 min. 7-AAD (BD Biosciences, 51-68981E) was added to the final suspensions before isolation of required single cells by FACS (Beckman moflo Astrios EQ). Cells (7-AAD-CD45-EpCAM+CD44+) sorted by FACS were then subjected to single-cell sequencing using a 10X Genomics platform. bioproject 741073 PRJNA741073 strain C57BL/6 age 8-week-old sex pooled male and female tissue the small intestine biomaterial_provider Shanghai SLAC Laboratory cell_type crypt cell collected_by Core facilities, Zhejiang university school of medicine treatment Cells (7-AAD-CD45-EpCAM+CD44+) sorted by FACS BioSampleModel Model organism or animal