a, Analysis of SSC1 and SSC2 showing expression of proliferation markers (left two panels), and the CBC signature (third from left), and individual CBC markers are overlaid on the crypt t-SNE graph (right three panels). n = 6,644 single-cell transcriptomes. b, Expression of indicated genes is plotted on a t-SNE graph of enriched crypts (n = 6,644 single-cell transcriptomes). c, Expression of Ly6a (also known as Sca-1) is shown in normal (top) and irradiated (bottom) cells of various enriched crypt clusters (n = 6,644 single-cell transcriptomes). d, Expression of indicated cell-type-specific genes is plotted across all enriched crypt clusters. Note that none of the differentiated lineage markers are enriched in SSC2. pct.exp, percentage of cells that express the gene; avg.exp.scale, scaled average expression of the gene; Pro., proliferating cells. e, Heat map showing differentially expressed genes in SSC2a–c. f, Expression of proliferation markers is overlaid on the SSC2 t-SNE map (n = 313 single-cell transcriptomes). g, Overlap between the top-50 SSC1 genes with SSC2a versus SSC2c is shown with a list of genes common to SSC1 and SSC2a. h, Analysis of zonation marker expression (as in Extended Data Fig. 2e). Note that SSC2a contains almost all the proliferative cells, overlaps extensively with SSC1 and CBC markers, and expresses crypt-specific genes. i, Expression of indicated genes identifying SSC2b, is overlaid on the crypt t-SNE plot (n = 6,644 single-cell transcriptomes). j, Clu expression is overlaid on the crypt t-SNE map (n = 6,644 single-cell transcriptomes). k, Dot plot showing scaled expression of Clu, Lgr5 and Ascl2 in the indicated SSC2 populations. Gene-expression values are shown as absolute (a, b, c, j, for individual genes) or median (a, f, i, for multiple genes) of log10(CPM).