a, Expression of the indicated YAP1-signature genes is overlaid on the crypt t-SNE plot. Gene expression is shown as median of log10(CPM). n = 6,644 single-cell transcriptomes. b, Endogenous Clu mRNA identified by smFISH (red) followed by visualization of E-cadherin-expressing epithelial cells by immunostaining (green) is shown in small intestine of wild-type or Yap1−/− mice at 3 dpi (n = 3 mice). c, Representative immunohistochemistry images of Clu-GFP transgene expression in 2 dpi wild-type or Yap1−/− small intestines, or in untreated Lats1−/−Lats2−/− (Lats1/2 KO) mutant small intestines (n = 2 mice). d, Analysis of proliferation in CLU+ cells. Representative images (left) of Clu-GFP expression (green) and EdU incorporation (red) at 3 dpi. Green arrowheads indicate GFP+EdU− cells, red arrowheads indicate GFP−EdU+ cells and yellow arrowheads indicate GFP+EdU+ cells (n = 65 images analysed). Pie graphs (right) show quantification of EdU+GFP− cells (top) and EdU+ cells in the GFP+ population (bottom). Note that GFP+ cells rarely display EdU incorporation. Scale bars, 35 μm (b–d).