Extended Data Fig. 9: Aberrant cell fate acquisition upon depletion of H3K27me3.

a, Brightfield images of organoids at day 15 treated with DMSO (control) or different concentrations of A395, an EED inhibitor. b, Western Blot of cellular extracts of 15 day old organoids shows depletion of H3K27me3 upon treatment with 1 µM A395. H3, β-Catenin and Ponceau serve as loading controls. This is a representative image of two replicates. The experiment has been performed 3 times on independent organoid batches. c, Heatmap of bulk H3K27me3 CUT&Tag signal on H3K27me3 peaks of two replicates of the inhibitor treatment ordered by intensity, showing consistent depletion of H3K27me3. d, Heatmap of bulk H3K27ac CUT&Tag signal on H3K27me3 peaks of two replicates of the inhibitor treatment ordered by intensity, showing consistent increase of H3K27ac. e, UMAP embedding colored by Louvain cluster annotation of the DMSO control and all inhibitor treated cells. f, UMAP embedding colored by expression of genes marking annotated Louvain clusters from (e). g, Barplot showing the log2 fold enrichment of different Louvain clusters over DMSO for the two replicates of the EED inhibitor treatment. Showing consistent trends between the experiments. h, Circular layout of differential transition probabilities between different cell states from the inhibitor treatment, showing an enrichment of H3K27me3 depleted cells at the terminal states of the graph (left), the circular plot colored by the expression of different marker genes (right) (see Methods ‘Inference of terminal fate probabilities in the perturbation experiment’ for details).