{"doi":"10.1101/2025.11.25.690485","title":"Evaluation of single-cell RNA profiling technologies using FFPE, fresh, and frozen ccRCC tumor specimens","abstract":"ABSTRACT The application of single-cell transcriptomic approaches has deepened our understanding of tumor heterogeneity, immune dynamics, and molecular programs underlying therapy response. The recent development of fixation-compatible single-cell platforms, such as 10x Genomics Flex, offers the opportunity to profile archived formalin-fixed, paraffin-embedded (FFPE) specimens, expanding access to clinically valuable samples. However, most benchmarking studies of recent single-cell RNA sequencing (scRNA-seq) technologies have relied on peripheral blood mononuclear cells, limiting their relevance to human tissues. Here, we compared three 10x single-cell RNA profiling methods, fresh tumor scRNA-seq, flash-frozen single-nucleus Multiome, and FFPE single-nucleus Flex (snFlex), using clear cell renal cell carcinoma (ccRCC) biopsies. Across methods, we observed broadly consistent cell type-specific transcriptional profiles among major ccRCC cell populations. Despite lower gene and UMI counts, snFlex reliably identified fine-grained states within CD8 + T cells, tumor-associated macrophages, and tumor compartments, comparable to those detected by scRNA-seq. Together, these findings highlight the distinct advantages of each technology depending on sample preservation type and study design, providing practical guidance for single-cell RNA profiling technology selection in translational studies using human tumor biopsies.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":583584,"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":0.8922,"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":55826,"name":"Sabrina Y. Camp","orcid":"0000-0002-9695-5527","position":1,"is_corresponding":false},{"id":419655,"name":"Amanda Garza","orcid":"0000-0001-8557-8765","position":2,"is_corresponding":false},{"id":933080,"name":"Yashika Rustagi","orcid":"0000-0003-1122-941X","position":3,"is_corresponding":false},{"id":615794,"name":"Erica Pimenta","orcid":"0000-0002-9684-6486","position":4,"is_corresponding":false},{"id":16398,"name":"Erin Shannon","orcid":"0000-0001-8112-2373","position":5,"is_corresponding":false},{"id":558516,"name":"Anwesha Nag","orcid":"0000-0002-1947-7429","position":6,"is_corresponding":false},{"id":1496551,"name":"Adam Betherman","orcid":null,"position":7,"is_corresponding":false},{"id":668438,"name":"Anthony Anselmo","orcid":"0000-0002-4761-1541","position":8,"is_corresponding":false},{"id":765407,"name":"Rachel Trowbridge","orcid":"0000-0003-4059-2031","position":9,"is_corresponding":false},{"id":55261,"name":"Aaron R. Thorner","orcid":"0000-0002-9160-7881","position":10,"is_corresponding":false},{"id":16400,"name":"Jihye Park","orcid":"0000-0002-4451-2046","position":11,"is_corresponding":false},{"id":16387,"name":"Kevin Bi","orcid":"0000-0002-6794-1804","position":12,"is_corresponding":false},{"id":418,"name":"Eliezer M. Van Allen","orcid":"0000-0002-0201-4444","position":13,"is_corresponding":false},{"id":1088558,"name":"Simayijiang Xirenayi","orcid":"0009-0000-1970-6554","position":0,"is_corresponding":true}],"reference_count":31,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:59:07.970345Z","pmid":"41394662","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":[]}