a, Plots of Clu-GFP+ and Lgr5-GFP+ quantification by FACS of single cells isolated from whole epithelium of the indicated mice analysed at different times after irradiation (n = 2 independent experiments with similar results). b, Gating strategy used to first select EPCAM+ epithelial cells and calculate percentage of Clu-GFP+ and Lgr5-GFP+ population within EPCAM+ epithelial cell fraction shown in Extended Data Fig. 4e. c, Gating strategy used to select healthy single cells for the above flow cytometry analyses. (related to a and b; n ≥ 3 mice each). d, Gating strategy used for flow cytometry-based purification of GFP+ and GFP− cells collected from enriched crypts of irradiated BAC-Clu-GFP mice for the Smart-Seq2 experiment shown in e−g (n = 2 mice). e, Violin plot of Clu expression, which represents distribution of expression intensity of individual Clu mRNA values in single GFP+ and GFP− epithelial cells purified in d and profiled by Smart-Seq2. f, t-SNE map of individual transcriptomes of Clu-GFP+ and Clu-GFP− (red and blue dots, respectively, in middle panel) cells purified as in d. Two distinct clusters identified by unsupervised analysis are marked (left, orange and light blue), and presence of cells in GFP+ versus GFP− populations are marked (middle). Expression of the indicated SSC2c signature is overlaid on the t-SNE plot (right). Gene-expression values (right) are shown as median of log10(CPM). g, Dot plot showing scaled expression of indicated SSC2c, proliferation, SSC2a, CBC and differentiated lineage markers in the clusters identified in f.