Fig. 2: scRNA-seq analysis reveals cellular diversity and cell fate dynamics in TpC-organoids. | Nature Communications

Fig. 2: scRNA-seq analysis reveals cellular diversity and cell fate dynamics in TpC-organoids.

From: A tunable human intestinal organoid system achieves controlled balance between self-renewal and differentiation

Fig. 2

a UMAP plot showing clustering of cells from scRNA-seq analysis of TpC organoids. Cluster labels indicate cell types. LGR5.high and LGR5.low indicate intestinal stem cells with different levels of LGR5 expression; TA1, transit-amplifying cell type 1; TA2, transit-amplifying cell type 2; Sec Pre, Secretory Precursor; Sec Pre2, Secretory Precursor Type 2; EC, enterocyte; EEC, enteroendocrine cell. b Proportion of each cell type from scRNA-seq sample in a. c Dot plot showing expression and percentage of cells expressing cell type-specific markers in clusters from scRNA-seq analysis. Dot size and color indicate normalized gene expression level. d UMAP plots showing expression of cell type-specific markers in TpC organoids. Color intensity indicates normalized gene expression level. e MA plot showing differentially expressed genes between Paneth cells and LGR5-high cells. f Heatmap showing predicted PROGENy pathway activity for each cell cluster. g UMAP plot showing subset analysis of secretory cells along with connected cell clusters. h Pie chart showing the proportion of each secretory cell type. Total percentages of all secretory cell types equal 100%. i Dot plot showing expression and percentage of cells expressing cell type-specific markers in clusters shown in g. Dot size and color indicate normalized gene expression level. j UMAP plots showing expression of cell type-specific markers in the secretory subset. Color intensity indicates normalized gene expression level. k UMAP plots highlighting EEC cells and depicting expression of EEC subtype-specific markers. Color intensity indicates normalized gene expression level. l PAGA trajectory analysis depicting cell connectivity. Circle size indicates cell number, and line thickness indicates connectivity strength between cell clusters. m RNA velocity analysis using Dynamo showing inferred transition direction between cell states. n Pie charts (top) showing proportions of indicated cell types among total cells, and bar charts (bottom) showing the composition of indicated cell types from scRNA-seq analysis of ES, IF, IL, TpC organoids, and crypt.

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