Supplementary Figure 6: Distinct and shared chromatin accessibility profiles of NK cells and CD8⁺ T cells during viral infection.

(A) Heatmap of all atlas peaks in NK and CD8⁺ T cells, including peaks that are unique to NK cells, unique to CD8⁺ T cells, and common between the two. (B) Principal component analysis of ATAC-seq on all common atlas peaks between NK cells and CD8⁺ T-cells. Normalized log₂ values were used for plotting. (C) Tabulation of differentially accessible (DA; FDR < 0.05; absolute log₂ fold change > 0.5; left) common atlas peak regions and differentially expressed (DE; FDR < 0.05; absolute log₂ fold change > 1; right) genes within categories defined by comparing memory and naïve cell states in both NK cells and CD8⁺ T cells. Common DA or DE regions are highlighted in gray. (D) Heatmap of DA atlas peaks in NK and CD8⁺ T cells, split by categories defined in (C). (E) Heatmap of DE genes in NK and CD8⁺ T cells, split by categories defined in (C). (F) Venn diagram of overlap between common DA gene loci (ATAC) and DE genes (RNA). P-values are calculated by hypergeometric test, using a union of all expressed genes and common atlas-assigned genes as background. (G) Gene expression from RNA-seq data of AP-1 transcription factor family genes plotted as log₂ transcripts-per-million (TPM) plus pseudocount of 1 shown as mean ± s.d. Dashed line shows count of 1. Gapdh and Cd4 are plotted as positive and negative controls, respectively.