BATF deficiency in ILCs alters heterogeneity of SI ILC3s. (A) UMAP plot of combined scRNA-seq data of SI-derived ILC3s from WT and littermate control cKO mice. Cells are colored by cluster. (B) Representative differentially expressed genes between clusters. Dot size represents the percentage of cells in a cluster expressing the gene and color shows the average relative expression of the gene. (C) UMAP representation of SI ILC3s isolated from WT and littermate control cKO mice. Cells are colored by cluster. (D) Pie charts displaying the proportion of subsets of ILC3s as described in C. (E and G) UMAP visualization showing a Th1 (E) and antigen presentation via MHCII signature (G) score on SI ILC3s as described in A. (F and H) GSEA for NK cell–mediated cytotoxicity (F) and antigen processing and presentation (H) signature genes in a given cluster compared to the rest of the cells. (I) Violin plots showing the expression of indicated genes among the three ILC3 clusters. (J and K) Violin plot showing Th1 (J) and antigen presentation via MHCII (K) signature score comparison between WT and cKO SI ILC3s. Two-sided Wilcoxon rank-sum tests were used (*P < 0.05, **P < 0.01, ***P < 0.001).