Protocol for preparation of mouse synovium for flow cytometry and RNA-seq

The mouse synovium can be used to model the sterile inflammation observed in rheumatoid arthritis and osteoarthritis. Here, we present a protocol for inducing arthritis and harvesting and preparing a single-cell suspension from cells of interest from the mouse synovium in steady state or inflammation, with or without intravascular labeling. The prepared single-cell suspension can then be used for downstream analyses, including flow cytometry, fluorescence-activated cell sorting (FACS), both bulk and single-cell RNA sequencing, and other genomic assays. For complete details on the use and execution of this protocol please refer to Montgomery et al.1 and Montgomery et al.2.