Extended Data Fig. 5: scRNA sequencing of SI organoids treated with DMSO or GW3965.

(a) Schematic of experimental strategy for scRNAseq. (b) Heatmap showing expression of top 25 differentially expressed marker genes for each cluster, with 5 DEG symbols noted per cluster. (c) Log-transformed expression of LXR target gene Abca1 in each cluster comparing DMSO and GW3965 treated organoids. (d) Cluster-wise cellular proportions comparing DMSO and GW3965 treated organoids. (e) Dot plot showing cluster-wise differentially expressed genes between organoids treated with either DMSO or GW3965. The colour intensity indicates the average logFC induction (top: genes upregulated in DMSO treated organoids; bottom: genes upregulated in GW3965-treated organoids) and the size of the dot indicates the p-value. Differences were considered significant at logFC>0.2, p < 0.01 and difference in proportion of expressing cells>0.2. (f) Relative fold-change of genes in Wnt, Notch and EGFR signalling modules in GW3965 treated organoids over DMSO in each cluster of the scRNAseq dataset. Data are produced from one experiment (a-f). Data are presented as mean ± s.e.m. (c). Significance was assessed by expression analysis with Wilcoxon rank-sum test (c, e, f). The schematic in panel a was drawn using BioRender.com.