Fig. 1. Study overview and open chromatin broad cell type identification.

a Study overview. Synovial biopsy specimens from RA and OA patients were utilized for unimodal scATAC-seq and multimodal snATAC-seq + snRNA-seq experiments. CITE-seq on similar specimens was performed in the AMP-RA reference study¹⁴. We defined chromatin classes using the unimodal scATAC-seq and multimodal snATAC-seq data and compared them with AMP-RA transcriptional cell states¹⁴ classified onto the multiome cells. We further defined transcription factors likely regulating these chromatin classes and found putative links to RA pathology by associating the classes to RA clinical metrics, RA subtypes, and putative RA risk variants. b Open chromatin broad cell type identification in unimodal scATAC-seq datasets (left) and multimodal snATAC-seq datasets (right) visualized on a UMAP, processed separately. Parts of Fig. 1a were generated using Servier Medical Art, provided by Servier, licensed under a Creative Commons Attribution 3.0 unported license.