Fig. 2: EBV-specific T cells of differing antigen specificities are distinguished in their chromatin accessibility landscapes.

A PCA of ATAC-seq data of CD8⁺ bulk subsets and tetramer-positive, EBV-specific CD8⁺ T cells. PCA is based on the 5000 most variable accessible sites across all groups. B K-means clustering of sites differentially accessible in any binary comparison across all groups. Peaks of each cluster were analyzed for transcription factor motif enrichment via HOMER. Key transcription factor families of enriched motifs are shown at the right margin. C, D Genes corresponding to peaks within each K-means cluster were identified via ChIPseeker. Only promoter and intergenic peak-associated genes were used to depict the top 5 peak-associated genes (as defined having the highest number of differential peaks in the corresponding K-means cluster) as well as for pathway and annotation enrichment. Selected ATAC-seq peak tracks are shown for K-means cluster 1 (C) and 5 (D). One-sided Fisher’s exact tests with Benjamini-Hochberg correction were used for enrichment analyses. Source data are provided as a Source Data file.