Transcriptomic analysis of synovial cells derived from collagen-induced arthritis mice

The destruction of bone and cartilage results in a loss of joint functionality, critically impairing the quality of life in arthritis patients. Synovial fibroblasts (SFs) critically contribute to the pathogenesis of rheumatoid arthritis (RA) by acquiring either a pro-inflammatory or tissue-destructive phenotype. To explore the molecular mechanisms underlying the pathogenic fibroblast phenotype in arthritis, we performed single-cell RNA sequencing (scRNA-seq) on the synovial cells which were isolated from collagen-induced arthritis (CIA) mice. Overall design: scRNA-seq analysis was performed on synovial cells which were isolated from the knee joints of CIA mice (n=3) and healthy control mice (n=9). Alignment, quantitation and aggregation of the sample count matrices (CIA + control) were performed using the 10x Genomics Cell Ranger pipeline (v.3.0) according to the manufacturer's protocol (GENEWIZ).