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Fig. 3 | BMC Biology

Fig. 3

From: Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types

Fig. 3

Single-cell RNA-sequencing reveals cellular composition across treatments and origins of proteomic data. a A tSNE plot of single cells derived from ENR + CV (n = 985 cells), ENR (n = 2544 cells), and ENR + CD (n = 2382 cells) harvested at day 6 of differentiation, colored by treatment; n = 6 wells for each condition. b Marker gene overlays (on plot from (a)) for binned count-based expression level (log(scaled UMI + 1)) of individual genes of interest. c A tSNE plot, with clusters identified through SNN graph-based clustering (see Additional file 1: Table S1 for marker gene lists), highlighting distinct cell states within each organoid; opacity of density clouds correspond to the Paneth cell score of ENR-4, ENR + CD-3, and ENR + CD-4 clusters (see Fig. 4b). d Violin plot of expression contribution to a cell’s transcriptome of ENR + CD proteome-enriched genes across organoid clusters from (c) (see Additional file 1: Table S1 for full gene list); effect size 2.40 ENR + CD-4 vs. all cells, p < 2.2 × 10−16. e Frequency of each cluster observed within each organoid condition as a fraction of the total cells in each condition

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