Extended Data Fig. 4: Deciphering inter-cell and intra-cell organoid heterogeneity.
a Characteristic organoid morphologies derived from four different transcriptional clusters as previously described15 (C2a, C2b, C2c, C1). Scale bars= 500 μm. b t-SNE plot clustering showing the individual organoid lines from Fig. 3h. c t-SNE plot clustering for the C2a and C2c organoids (n = 2015 organoids) superimposed on the Extended Data Fig. 4b. d Organoid phenotypes (n = 588 organoids) from epithelial and mesenchymal type of organoids derived from various mouse models (with different driver mutations): Ptf1aCre/+; Pi3kca+H1047R/+ (n = 6 mouse lines, note that the line E248 is not forming 3D organoids), Pdx1Cre/+; KrasG12D/+; TP53 ΔHO (n = 6 mouse lines), Ptf1aCre/+; KrasG12D/+; Cdkn2a ΔHO (n = 6 mouse lines). Scale bars= 500 μm. e Schematic representation of the morphological clone isolation and expansion. Image created with BioRender.com. f Major 3D morphological families that were used for further characterisation. Scale bars= 500 μm. g Extreme Limiting Dilution Analysis (ELDA) of epithelial and mesenchymal organoid phenotypes. h Log plot of nonresponding wells vs cell dosage for the epithelial (left) and mesenchymal (right) 3D organoid phenotypes. i Proliferation rate as % compared to the bulk population for the epithelial (from the mouse line ID: 9591 from 3 individual experiments) and mesenchymal (from the mouse line ID: 16992 from 3 individual experiments) 2D clones. Unpaired two-tailed parametric t-test with Welch’s correction, two-tailed. Both graphs represent mean±sem. j Heatmap of signature genes from E and M organoid phenotypes.
