Extended Data Fig. 6: Oncogene-driven signalling changes.
From: Tracing oncogene-driven remodelling of the intestinal stem cell niche
a, FACS sorting strategy to isolate cells from Confetti and Red2Onco tissue. R1, live; R2, singlet; R3, mesenchymal/immune (EPCAM−); R4, epithelial (EPCAM+); R5, mutant-epithelial (RFP+); R6, WT epithelial (YFP+); R7, immune (CD45+); R8, mesenchymal (CD45−). b, Box plots showing distributions of Pearson correlation coefficients in averaged log2-transformed normalized UMIs for cell types across all pairs of mice from the same (white) and between different (grey) conditions. c, UMAP of epithelial cells detected by Louvain. k, k nearest-neighbour value. d, UMAPs showing distribution of averaged expression of marker genes. Colour bars, average log2-transformed normalized UMIs. Top left from Fig. 3b. e, Heat map representing marker expression for epithelial cells. Coloured panel (left) groups marker genes (right) for cell types. Colour bar, auto-scaled log2-transformed normalized UMIs. f, Heat maps representing differential gene expression for epithelial cells in Red2Onco compared to Confetti. Parentheses, number of differentially expressed genes. Colour bar, log2(fold change) (Supplementary Table 1). g, UMAPs showing distributions of mutant (RFP+) and WT (YFP+) epithelial cells for Confetti and Red2Onco mice. h, i, Fractions of mutant (h) and WT (i) epithelial cells in Red2Onco and Confetti mice. See Fig. 3c for other WT data. j–l, Confocal images (j) of EGFP+ cells, representative of tissues quantified for stem cell number (k) and fraction (l). In j, white arrows indicate WT crypts proximate to mutant (MT) crypts. White dashed lines mark crypts. Scale bars, 25 μm. m, n, FACS plots (m) and quantification (n) of EGFPhi stem cell fractions from R5 or R6 (a). Small intestine from Lgr5-EGFP-IRES-CreERT2;Red2Onco 2 w after induction (clonal dosage (0.2 mg per 20 g body weight) for j–l, mosaic dosage (4 mg per 20 g body weight) for m, n). *P < 0.05, **P < 0.01, ***P < 0.0001; n.s., statistically not significant, P > 0.05; two-sided Kolmogorov–Smirnov test (b), two-sided likelihood ratio test (h, i) and one-way ANOVA with Games-Howell’s multiple comparisons test (k, l, n). Data are mean ± s.e.m. (h, i, k, l) or mean ± s.d. (n). For exact P values, see Source Data.
