Fig. 6.

RA endothelial chromatin classes.

a. UMAP colored by 4 endothelial 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 SOX17 motif (left). Most significantly enriched motifs in marker peaks per endothelial 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(padj) value shown in parentheses in motif label. P-values were calculated via hypergeometric test in ArchR³². E_A-3 is not shown because only 1 marker peak was found, likely due to low cell counts.

d. UMAP colored by NES normalized gene expression (left). NES locus (chr1:156,675,399-156,680,400) 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).