Fig. 1

scRNA-seq analysis of a mouse model of antigen-induced arthritis (AIA). a An overview of the AIA mouse model. b Representative joint images from naïve mice and arthritic joints after hematoxylin and eosin (H&E) staining. B, bone marrow; S, synovial cavity; C, cartilage. Arrows indicate (1) infiltration of inflammatory cells to the synovium, (2) cartilage/bone destruction, and (3) hyperplasia of the synovial lining. c A schematic overview of seq-well scRNA-seq and cell type identification using reference component analysis (RCA). d t-SNE plot of 7086 healthy and RA joint cells (n = 4 healthy mice samples and 5 sick mice samples), and 1333 healthy and AIA lymph nodes cells (n = 4 healthy mice samples and 5 sick mice samples), colored by RCA clusters