{"doi":"10.1038/s41586-024-08172-8","title":"An integrated transcriptomic cell atlas of human neural organoids","abstract":"Human neural organoids, generated from pluripotent stem cells in vitro, are useful tools to study human brain development, evolution and disease. However, it is unclear which parts of the human brain are covered by existing protocols, and it has been difficult to quantitatively assess organoid variation and fidelity. Here we integrate 36 single-cell transcriptomic datasets spanning 26 protocols into one integrated human neural organoid cell atlas totalling more than 1.7 million cells<sup>1-26</sup>. Mapping to developing human brain references<sup>27-30</sup> shows primary cell types and states that have been generated in vitro, and estimates transcriptomic similarity between primary and organoid counterparts across protocols. We provide a programmatic interface to browse the atlas and query new datasets, and showcase the power of the atlas to annotate organoid cell types and evaluate new organoid protocols. Finally, we show that the atlas can be used as a diverse control cohort to annotate and compare organoid models of neural disease, identifying genes and pathways that may underlie pathological mechanisms with the neural models. The human neural organoid cell atlas will be useful to assess organoid fidelity, characterize perturbed and diseased states and facilitate protocol development.","journal":"Nature","year":2024,"id":10855,"datarank":1.7928011542818016,"base_score":4.51085950651685,"endowment":4.51085950651685,"self_citation_contribution":0.6766289259775276,"citation_network_contribution":1.116172228304274,"self_endowment_contribution":0.6766289259775276,"citer_contribution":1.116172228304274,"corpus_percentile":63.71033360455655,"corpus_rank":447,"citation_count":111,"citer_count":93,"citers_with_citation_signal":58,"citers_with_endowment":58,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.8956,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-11-20","fair_score":49.7917,"fair_percentile":77.9023746701847,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":12138,"name":"Leander Dony","orcid":"0000-0001-5697-6991","position":1,"is_corresponding":false},{"id":40551,"name":"Jonas Simon Fleck","orcid":"0000-0002-4686-7254","position":2,"is_corresponding":false},{"id":22110,"name":"Artur Szalata","orcid":"0000-0001-8413-234X","position":3,"is_corresponding":false},{"id":40552,"name":"Katelyn X. Li","orcid":"0000-0001-8799-0534","position":4,"is_corresponding":false},{"id":40553,"name":"Irena Slišković","orcid":"0009-0003-6222-7657","position":5,"is_corresponding":false},{"id":40555,"name":"Malgorzata Santel","orcid":"0009-0006-4947-8509","position":7,"is_corresponding":false},{"id":40556,"name":"Alexander Atamian","orcid":"0009-0004-5525-2018","position":8,"is_corresponding":false},{"id":40557,"name":"Giorgia Quadrato","orcid":"0000-0003-0717-4874","position":9,"is_corresponding":false},{"id":40558,"name":"Jieran Sun","orcid":"0000-0002-7996-3840","position":10,"is_corresponding":false},{"id":40559,"name":"Sergiu P. Pașca","orcid":"0000-0002-3216-3248","position":11,"is_corresponding":false},{"id":40560,"name":"Human Cell Atlas Organoid Biological Network","orcid":null,"position":12,"is_corresponding":false},{"id":40561,"name":"Neal D. Amin","orcid":"0000-0003-2027-1329","position":13,"is_corresponding":false},{"id":40562,"name":"Kevin W. Kelley","orcid":null,"position":14,"is_corresponding":false},{"id":40563,"name":"Taylor Bertucci","orcid":"0009-0008-1017-6807","position":15,"is_corresponding":false},{"id":40564,"name":"Sally Temple","orcid":"0000-0001-7301-783X","position":16,"is_corresponding":false},{"id":40565,"name":"Kathryn R. Bowles","orcid":null,"position":17,"is_corresponding":false},{"id":40567,"name":"Emanuele Villa","orcid":null,"position":19,"is_corresponding":false},{"id":40568,"name":"Giuseppe Testa","orcid":"0000-0002-9104-0918","position":20,"is_corresponding":false},{"id":13070,"name":"Cristiana Cruceanu","orcid":"0000-0002-7799-5531","position":21,"is_corresponding":false},{"id":5365,"name":"Elisabeth B. Binder","orcid":"0000-0001-7088-6618","position":22,"is_corresponding":false},{"id":29631,"name":"J. Gray Camp","orcid":"0000-0003-3295-1225","position":23,"is_corresponding":false},{"id":42,"name":"Fabian Joachim Theis","orcid":"0000-0002-2419-1943","position":24,"is_corresponding":false},{"id":29636,"name":"Barbara Treutlein","orcid":"0000-0002-3299-5597","position":25,"is_corresponding":false},{"id":40569,"name":"Hsiu‐Chuan Lin","orcid":"0000-0001-9587-6483","position":26,"is_corresponding":false},{"id":40570,"name":"Carlo Emanuele Villa","orcid":"0000-0002-1208-3160","position":27,"is_corresponding":false},{"id":40550,"name":"Zhisong He","orcid":"0000-0002-1502-4801","position":0,"is_corresponding":true}],"reference_count":100,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"39567792","pmcid":"PMC11578878","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"hybrid","license":"cc-by-nc-nd","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":65.0,"fair_a":67.5,"fair_i":25.0,"fair_r":41.6667,"fair_zscore":0.4143,"fair_rationale":{"fair_score":49.79,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":65.0,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"datacite=0, pmcid=True, pmid=True","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers 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statements link to Zenodo, CellxGene, and a web portal for browsing and mapping, but the text does not specify any access restrictions or a formal authentication/authorization protocol."}]},"I":{"name":"Interoperable","score":25.0,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"linked_datasets=0, datacite=0","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null},{"key":"i_standards","label":"Standard formats, vocabularies & identifiers","kind":"llm","weight":1.0,"fraction":0.5,"signal":null,"rationale":"The paper uses standard single-cell formats (AnnData, h5ad) and common vocabularies (e.g., cell type names, gene symbols), but does not mention use of persistent identifiers (e.g., DOIs for datasets) or community standard ontologies 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and lack of explicit reproducibility instructions for the entire analysis reduce the reusability score."}]}},"suggestions":["Include machine-readable metadata in JSON-LD or RDFa format directly in the article or as a structured data file.","Specify a formal access protocol (e.g., OAuth, API token) if data access requires authentication, or state 'no restrictions' clearly.","Assign persistent identifiers (e.g., DOIs) to all datasets and use ontology terms (e.g., UBERON, CL) for cell types and anatomical regions in the manuscript.","Provide a more permissive license (e.g., CC BY 4.0) to maximize reuse and explicitly outline steps to reproduce all figures and tables.","Add a reproducibility section or containerized environment (e.g., Docker/Singularity) with exact software versions for the full analysis 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