Fig. 4: scRNA-seq profiling of enteroids cultured with rimonabant/SP600125 or AS1842856.

a Uniform manifold approximation and projection (UMAP) visualization of 14,767 cells summarizing enteroid differentiation from all samples, color labeled by culture condition. b UMAP visualization from a, color labeled by broad annotated cell identity, following Louvain clustering. c Dot plot of the average scaled expression (measured by average Pearson residual) of canonical markers of various intestinal epithelial cell types, plotted against cluster identity. d Proportional abundance of epithelial cell subsets by enteroid culture protocol. Each culture condition consists of three different enteroid lines from distinct human donors, as denoted by data point shape. Bars show mean ± SEM; Kruskal-Wallis test with Dunn’s post-hoc analysis displayed. P values were adjusted using Bonferroni correction for multiple comparisons. *p = 0.0219 (Intestinal Stem Cells and Enteroendocrine Cells), 0.0338 (Enterocytes). e UMAP visualization of 14,767 cells divided by culture condition and colored by cell identity. Trajectory analysis of each protocol was calculated using scVelo and the vector field was overlaid on top of each UMAP. Arrows represent smoothed averages of the estimated cellular differentiation trajectory, with arrow thickness corresponding to the “speed” of differentiation. f UMAP visualization from a, with individual cells colored by their EE cell module score. Each score was scaled on a range from 0 to 1. g Violin plots of the module score described in f split across culture condition. The effect size between culture conditions was calculated as Cohen’s d; $$0.8 < d < 1.2. Source data are provided as a Source Data file.