Extended Data Fig. 6: CLU⁺ cells are produced in a YAP1-dependent manner and are quiescent.

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).