Fig. 2.

RA T cell chromatin classes.

a. UMAP colored by 5 T cell chromatin classes defined from unimodal scATAC and multimodal snATAC cells.

b. Binned normalized marker peak accessibility (top) and gene expression (bottom) for multiome snATAC cells on UMAP.

c. UMAP colored by chromVAR³¹ deviations for the TBX21 motif (left). Most significantly enriched motifs in marker peaks per T cell chromatin class (right). To be included per class, motifs had to be enriched in the class above a minimal threshold and corresponding TFs had to have at least minimal expression in snRNA (Methods). Color scale normalized per motif across classes with max −log10(p_adj) value shown in parentheses in motif label. P-values were calculated via hypergeometric test in ArchR³².

d. UMAP colored by KLRG1 normalized gene expression in multiome cells (left). KLRG1 locus (chr12:8,987,550-8,990,000) with selected isoforms, motifs, open chromatin peaks, and chromatin accessibility reads from unimodal and multimodal ATAC cells aggregated by chromatin class and scaled by read counts per class (Methods) (right).