{"doi":"10.7554/elife.70692","title":"RNA splicing programs define tissue compartments and cell types at single-cell resolution","abstract":"The extent splicing is regulated at single-cell resolution has remained controversial due to both available data and methods to interpret it. We apply the SpliZ, a new statistical approach, to detect cell-type-specific splicing in >110K cells from 12 human tissues. Using 10X Chromium data for discovery, 9.1% of genes with computable SpliZ scores are cell-type-specifically spliced, including ubiquitously expressed genes MYL6 and RPS24 . These results are validated with RNA FISH, single-cell PCR, and Smart-seq2. SpliZ analysis reveals 170 genes with regulated splicing during human spermatogenesis, including examples conserved in mouse and mouse lemur. The SpliZ allows model-based identification of subpopulations indistinguishable based on gene expression, illustrated by subpopulation-specific splicing of classical monocytes involving an ultraconserved exon in SAT1 . Together, this analysis of differential splicing across multiple organs establishes that splicing is regulated cell-type-specifically.","journal":"eLife","year":2021,"id":152437,"datarank":1.5806851990485917,"base_score":4.330733340286331,"endowment":4.330733340286331,"self_citation_contribution":0.6496100010429497,"citation_network_contribution":0.9310751980056419,"self_endowment_contribution":0.6496100010429497,"citer_contribution":0.9310751980056419,"corpus_percentile":null,"corpus_rank":null,"citation_count":75,"citer_count":55,"citers_with_citation_signal":45,"citers_with_endowment":45,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9241,"is_data_producer":true,"deposit_databanks":{"GEO":["SRR6459190","SRR6459191","SRR6459192","SRR6459155","SRR6459156","SRR6459157"],"figshare":["10.6084/m9.figshare.14531721"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":74091,"name":"Roozbeh Dehghannasiri","orcid":"0000-0001-7413-3437","position":1,"is_corresponding":false},{"id":252038,"name":"Peter L. Wang","orcid":"0000-0001-9651-3860","position":2,"is_corresponding":false},{"id":74025,"name":"SoRi Jang","orcid":"0000-0002-9156-552X","position":3,"is_corresponding":false},{"id":74128,"name":"Antoine de Morrée","orcid":"0000-0002-8316-4531","position":4,"is_corresponding":false},{"id":74002,"name":"Serena Y. Tan","orcid":"0000-0001-5409-0695","position":5,"is_corresponding":false},{"id":647559,"name":"Jingsi Ming","orcid":"0000-0001-7059-4156","position":6,"is_corresponding":false},{"id":647560,"name":"Angela Ruohao Wu","orcid":"0000-0002-3531-4830","position":7,"is_corresponding":false},{"id":11049,"name":"Stephen R. Quake","orcid":"0000-0002-1613-0809","position":8,"is_corresponding":false},{"id":104362,"name":"Mark A. Krasnow","orcid":"0000-0002-1976-5471","position":9,"is_corresponding":false},{"id":558818,"name":"Julia Salzman","orcid":"0000-0001-7630-3436","position":10,"is_corresponding":false},{"id":74138,"name":"Julia Olivieri","orcid":"0000-0002-0850-5498","position":0,"is_corresponding":true}],"reference_count":60,"raw_metadata":null,"created_at":"2026-07-18T23:43:34.972031Z","pmid":"34515025","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":[]}