{"doi":"10.1016/j.xpro.2025.104277","title":"Protocol to evaluate mouse brain spatial cell type-resolved transcriptomic discoveries using 10× Visium spatial transcriptomics and FLEX scRNA-seq","abstract":"Understanding changes in gene expression and cell-cell signaling among spatial regions in diseased tissues adds critical biological information to understanding mechanisms. Here, we present a protocol to investigate molecular transcriptional drivers within intact murine tissue using 10× Genomics Visium spatial transcriptomics and 10× Genomics FLEX single-cell RNA sequencing (scRNA-seq) data. We describe steps for collecting mouse brain tissue from multiple ages, processing samples, and mounting the tissue. We then detail procedures for staining, FLEX tissue section collection, fixation, dissociation, and cell storage. For complete details on the use and execution of this protocol, please refer to Burns et al. 1 • Mouse brain collection at multiple time points for spatial transcriptomics and scRNA-seq • Steps for fresh frozen spatial tissue processing with Visium and FLEX scRNA-seq • Processing of postnatal day 0 mouse brain tissue for sequencing Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Understanding changes in gene expression and cell-cell signaling among spatial regions in diseased tissues adds critical biological information to understanding mechanisms. Here, we present a protocol to investigate molecular transcriptional drivers within intact murine tissue using 10× Genomics Visium spatial transcriptomics and 10× Genomics FLEX single-cell RNA sequencing (scRNA-seq) data. We describe steps for collecting mouse brain tissue from multiple ages, processing samples, and mounting the tissue. We then detail procedures for staining, FLEX tissue section collection, fixation, dissociation, and cell storage.","journal":"STAR Protocols","year":2025,"id":529641,"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":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.783,"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":297949,"name":"Ricardo Miramontes","orcid":"0000-0002-9231-2479","position":1,"is_corresponding":false},{"id":878953,"name":"John C. Reidling","orcid":null,"position":2,"is_corresponding":false},{"id":297944,"name":"Ryan G. Lim","orcid":"0000-0001-6388-5158","position":3,"is_corresponding":false},{"id":231741,"name":"Leslie M. Thompson","orcid":"0000-0003-4573-9514","position":4,"is_corresponding":false},{"id":697524,"name":"Mara S. Burns","orcid":null,"position":0,"is_corresponding":true}],"reference_count":14,"raw_metadata":null,"created_at":"2026-07-19T02:50:56.971987Z","pmid":"41456279","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":[]}