a, Irradiation-induced changes in the cellular composition of the indicated intestinal epithelial cell types are plotted as per cent of untreated controls. b, Frequency plot of Lgr5 expression levels in individual cells of the indicated samples. Note that radiation depletes Lgr5high cells in both whole epithelia and enriched crypt samples. c, Representative images of untreated and irradiated small intestines stained for CD45 (red), EPCAM (green), and counterstained for DAPI (blue). Note that CD45+ immune cells infiltrate crypts upon irradiation (n = 3 mice each). d, Number of cells in the EC and CBC clusters from untreated (blue) or irradiated (red) intestines. e, Regional distribution of ECs and CBCs. scRNA-seq data from the indicated cell clusters were compared to zonation markers and transcriptional overlap between marker genes of the indicated individual CBC and EC clusters, and zone-specific gene signatures (see Methods) plotted as percentage. f, Regional distribution of intestinal epithelial cells. Number of CBCs (red) and all ECs (blue) that display the indicated zonation markers18 without (darker) or with (lighter) irradiation. Scale bar, 75 μm.