{"doi":"10.1016/j.xpro.2025.104207","title":"Protocol for preparation of mouse synovium for flow cytometry and RNA-seq","abstract":"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 • Steps for the isolation of synovial cells from mouse joints • Preparation of a single-cell suspension from synovial tissue • Staining for profiling of immune cell populations with intravascular labeling Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. 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.","journal":"STAR Protocols","year":2025,"id":581335,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9433,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":456355,"name":"Carla M. Cuda","orcid":"0000-0002-2022-8171","position":1,"is_corresponding":false},{"id":456353,"name":"Salina Dominguez","orcid":"0009-0002-2659-7610","position":2,"is_corresponding":false},{"id":456348,"name":"Hadijat M. Makinde","orcid":"0000-0001-8492-4187","position":3,"is_corresponding":false},{"id":1699,"name":"Alexander V. Misharin","orcid":"0000-0003-2879-3789","position":4,"is_corresponding":false},{"id":301554,"name":"Yidan Wang","orcid":"0000-0003-2490-8999","position":5,"is_corresponding":false},{"id":1492969,"name":"A. Sanz Miguel","orcid":null,"position":6,"is_corresponding":false},{"id":456349,"name":"Deborah R. Winter","orcid":"0000-0003-1806-673X","position":7,"is_corresponding":false},{"id":226246,"name":"Harris Perlman","orcid":"0000-0003-4174-608X","position":8,"is_corresponding":false},{"id":385262,"name":"Anna B. Montgomery","orcid":"0000-0002-7019-4299","position":0,"is_corresponding":true}],"reference_count":2,"raw_metadata":null,"created_at":"2026-07-19T02:58:47.357782Z","pmid":"41236928","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}