H3K4me3 ChIP-seq peak calling and atlas generation.

Peak calling was performed on each IP-input paired sample with MACS2, with arguments ‘– BAMPE –q 0.05’. Peaks that exhibited a q value score higher than the 25th percentile were retained. Samples that yielded >6,000 of these filtered peaks were merged to generate a union of all lists, with overlapping ranges combined into a single feature that fully encompassed each overlapping peak. For each analysis, a separate peak atlas was produced based on samples relevant to that analysis. For in vivo atlas, only in vivo samples were included to generate the atlas. For in vitro cytokine-stimulated samples, two sets of samples were included for atlas generation based on the comparisons that were performed: one comparing only IFN-α induced H3K4me3 histone modifications in WT and Stat1^−/− NK cells and the other comparing IFN-α, IL-12/IL-18, IL-2/IL-15 or a combination of the three in only WT samples. In both cases, unstimulated samples were included only if a paired stimulated sample relevant to the analysis was also available. Thus three separate atlases were generated, one provided in Supplementary Table 3 for the STAT1KO NK cells and the other two incorporated into the merged atlas in Supplementary Table 6.