Extended Data Fig. 6: Perturbation of crypt clustering in ISC-Cre mice.

a, PCR genotyping of genomic DNA for Apc exon 14 shows the excised product (240 bp) in FACS-purified ISCs (Tom⁺ cells) from ISC-Cre mice treated with 0.1 mg Tam (N = 2 mice) but not in ISCs purified from animals that did not receive Tam (N = 2 mice). Purified Tom^- and Tom⁺ crypt cell fractions from mice treated with 1 mg Tam (Extended Data Fig. 2g) serve as negative and positive controls. Whole gel is shown; a larger non-specific PCR product is amplified in all samples. b, In situ hybridization revealed Notum expression in clonal structures in ISC-Cre;Apc^fl/fl ileum after 2 doses of 0.1 mg Tam (N = 2 mice). Top: low magnification, bottom (2 images): high magnification; all scale bars 50 μm. c, Monte Carlo simulations revealed high clustering after ISC-Cre mice were treated with 0.1 mg Tam, as expected from the underlying patchy variegation, but cluster sizes were substantially reduced compared to mice treated with 1 mg Tam. Cumulative frequencies compared with others in Fig. 3g; dark grey: 5^th to 95^th percentile range, light grey: maximum range for simulated data. Note different y-axis ranges for 1 mg and 0.1 mg treatments; circled dots: measured clustering frequencies. d, Sparse crypt labelling detected in ISC-Cre Apc^Fl/Fl ileum whole mounts 5 days PCI with 0.1 mg Tam. N = 3 mice, scale bar 1 cm. e, Whole ISC-Cre;Apc^Fl/Fl ileum 8 weeks (N = 4 mice) and 23 weeks (N = 2 mice) PCI after 0.1 mg Tam, showing small discrete adenomas (dashed ovals) in one of the latter ilea. Scale bars 1 cm.