Fig. 4
From: Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types
Transcriptional identity of chemically induced Paneth cells (CI-PCs) within conditions and related to in vivo PCs. a Violin plots for the count-based expression level (log(scaled UMI + 1)) of selected genes across called clusters, colors correspond to clusters in Fig. 4c; *t test, p < 6.80 × 10−74 or less with Bonferroni correction, for Lyz1, Defa24, Defa3, and Mmp7 ENR + CD-4 relative to ENR-4. b Violin plot of expression contribution to a cell’s transcriptome of in vivo PC and enteroendocrine marker-cell genes (see Additional file 1: Table S1 for full gene list, AUC > 0.65); effect size 2.52 ENR + CD-4 vs. ENR-4, p < 2.2 × 10−16 for PC score; effect size 0.0465, p = 0.2339 ENR + CD-4 vs. ENR-4 for enteroendocrine cell score. c Row-clustered heatmap of z-scores (−2.5 to 2.5; purple to yellow) for defining genes (n = 69 with AUC > 0.65 of in vivo PCs, see Additional file 1: Table S1 for full gene list) across top 200 cells for PC score (Fig. 5b) from ENR-4 and ENR + CD-4 conditions compared to two biological replicates of in vivo PCs from the terminal ileum (n = 196 cells)