Supplementary Figure 4: Related to Supplementary Figure 5. Memory ILC1 have distinct transcriptome and epigenomes compared to naïve ILC1.

(a) Gene set enrichment analysis (GSEA) of genes upregulated in D35 IL-18rα⁺ ILC1 over D0 ILC1 from genes upregulated in effector memory T cells (T_EM) (left) or resident memory T cells (T_RM) (right) compared to naïve T cells after LCMV infection, assessed by RNAsequencing as was previously reported³². (NES, normalized enrichment score; FDR, false discovery rate; NES, normalized enrichment score assessed by an empirical phenotype based permutation test assuming a null distribution). (b) Absolute numbers and proportion of all peaks (23016 total) and differentially accessible (DA) peaks in peak atlas (373 total, p value less than 0.2). (c) MA plots of differentially accessible regions (red dots) of all peak types comparing D0 vs D35 IL-18rα⁺ ILC1. (d) Representative ATAC-sequencing tracks show accessible regions for Rora, Itgb3, and Il7r in naïve and memory ILC1. Y axis depicts normalized counts, while X axis displays genomic axis with scale bar. Data are representative of 2 replicate experiments with n=2 samples of n=20 mice per condition. All adjusted p values were indeed determined using DESeq2 and were two-sided.