BATF regulates the SI ILC3 transcriptional program. (A) Heatmap of bulk RNA-seq data showing significantly upregulated (1,380) and downregulated (3,368) genes of SI ILC3s from cKO and littermate control WT mice. (B) Heatmaps of expression of genes involved in MHCII antigen presentation from cKO versus WT SI ILC3s. (C–E) GSEA of selected pathways enriched in WT (C and D) and cKO (E) SI ILC3s. Normalized enrichment scores (NES) and adjusted P values are indicated for each gene set. (F) Heatmaps of expression of genes involved in type 1 effector genes from cKO versus WT SI ILC3s. (G) Representative flow plots of SI ILC3s (Lin⁻CD90.2⁺RORγt⁺) of WT and littermate control cKO mice. (H) Representative percentage (upper panel) and quantification of mean fluorescence intensity (MFI; bottom panel) of indicated markers on or in SI ILC3 of WT and littermate control cKO mice. (I and K) Representative flow plots of intracellular staining of IFN-γ–expressing ILC3s isolated from SI (I) and LI (K) of WT and littermate control cKO mice after stimulation with PMA plus ionomycin ex vivo. FSW, forward side pulse width. (J and L) Quantification of the frequency of IFN-γ⁺ ILC3s from SI (J) and LI (L). Data are shown as mean ± SEM. *P < 0.05, **P < 0.01, ***P < 0.001 (two-tailed unpaired t test). Each dot represents one mouse, n = 4–6 mice per group. Data are pooled from two independent experiments. See also Fig. S5.