{"doi":"10.1016/j.crmeth.2023.100548","title":"Single-cell sequencing of individual retinal organoids reveals determinants of cell-fate heterogeneity","abstract":"models of human development and disease, organoids hold immense potential. Their complex cellular composition makes single-cell sequencing of great utility; however, the limitation of current technologies to a handful of treatment conditions restricts their use in screens or studies of organoid heterogeneity. Here, we apply sci-Plex, a single-cell combinatorial indexing (sci)-based RNA sequencing (RNA-seq) multiplexing method to retinal organoids. We demonstrate that sci-Plex and 10× methods produce highly concordant cell-class compositions and then expand sci-Plex to analyze the cell-class composition of 410 organoids upon modulation of critical developmental pathways. Leveraging individual organoid data, we develop a method to measure organoid heterogeneity, and we identify that activation of Wnt signaling early in retinal organoid cultures increases retinal cell classes up to 6 weeks later. Our data show sci-Plex's potential to dramatically scale up the analysis of treatment conditions on relevant human models.","journal":"Cell Reports Methods","year":2023,"id":324739,"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":33,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9351,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1029445,"name":"Akshayalakshmi Sridhar","orcid":"0000-0002-6873-0398","position":1,"is_corresponding":false},{"id":374756,"name":"Kiara C. Eldred","orcid":"0000-0002-4067-8639","position":2,"is_corresponding":false},{"id":1041494,"name":"Sophia A. Cuschieri","orcid":"0009-0005-7260-5062","position":3,"is_corresponding":false},{"id":1042215,"name":"Dawn Hoffer","orcid":null,"position":4,"is_corresponding":false},{"id":19437,"name":"Cole Trapnell","orcid":"0000-0002-8105-4347","position":5,"is_corresponding":false},{"id":90383,"name":"Thomas A. Reh","orcid":"0000-0002-3524-0886","position":6,"is_corresponding":false},{"id":268501,"name":"Amy Tresenrider","orcid":"0000-0002-0819-9187","position":0,"is_corresponding":true}],"reference_count":64,"raw_metadata":null,"created_at":"2026-07-19T01:08:16.809511Z","pmid":"37671011","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":[]}