Extended Data Fig. 8: Multiomic sequencing comparison of in vitro SC-islets and transplanted in vivo SC-islets.
a, Integrative UMAP clustering showing cells from in vitro SC-islets and in vivo SC-islets using gene expression and chromatin information (36688 cells from 6 independent biological samples; 3 in vitro SC-islets, 3 in vivo SC-islets; integration of all samples). The pie chart shows composition of cell types in each condition. b, UMAP showing distribution of SC-islet cells from in vitro or after transplanted in vivo condition. This plot highlights the separation of clusters from transplanted in vivo SC-β and SC-EC cells. c, Differential gene expression analysis (top) and motif chromatin accessibility analysis (bottom) of SC-β, SC-α, SC-δ and SC-EC cell populations from in vitro SC-islets and in vivo SC-islets. Statistical significance was assessed by two-sided Wilcoxon rank sum test for RNA expression and two-sided logistic regression for motif chromatin accessibility. d, Gene set enrichment analysis showing enrichment of gene sets comparing in vitro SC-β cells and vivo SC-β cells. Non-adjusted p-values were computed using two-sided Fisher exact test. e, Bar graphs showing fold change differences of cell type associated active transcription factors in SC-α, SC-δ and SC-EC cells from in vitro and in vivo conditions. f, Heatmap comparing gene expression, promoter accessibility, or motif chromatin accessibility in β-cells from in vitro SC-islets, in vivo islets, and primary islets (26697 cells from 5 independent biological samples; 1 representative in vitro SC-islets, 1 representative primary islets, 3 in vivo SC-islets). EC, enterochromaffin.
