library_construction_protocol: Intestinal crypts were isolated according to standard protocol. Briefly, intestines were flushed with cold PBS, incubated in EDTA buffer and full intestinal crypts were dissociated in single cells with collagenase dispase solution. Subsequently, single cells were sorted for DAPI-negative to select for live cells, Epcam-positive to acquire epithelial cells, CD45-negative to exclude lymphocytes and CD31-negative to exclude endothelial cells. After sorting, cells were pelleted and re-suspended in 1000cells/ul final concentration and cell viability was assessed as a quality check parameter. Only samples with viabilities higher tan 85% were processed for library preparation, which was done using 10X_3primer_mRNA as per manufacturer's instructions.