Single-cell sequencing has revolutionized the scale and resolution of molecular profiling of tissues and organs. Here, we present an integrated multimodal reference atlas of the most accessible portion of the mammalian central nervous system, the retina. We compiled around 2.4 million cells from 55 donors, including 1.4 million unpublished data points, to create a comprehensive human retina cell atlas (HRCA) of transcriptome and chromatin accessibility, unveiling over 110 types. Engaging the retina community, we annotated each cluster, refined the Cell Ontology for the retina, identified distinct marker genes, and characterized cis-regulatory elements and gene regulatory networks (GRNs) for these cell types. Our analysis uncovered intriguing differences in transcriptome, chromatin, and GRNs across cell types. In addition, we modeled changes in gene expression and chromatin openness across gender and age. This integrated atlas also enabled the fine-mapping of GWAS and eQTL variants. Accessible through interactive browsers, this multimodal cross-donor and cross-lab HRCA, can facilitate a better understanding of retinal function and pathology.
","journal":null,"year":2023,"id":11563,"datarank":0.5653180390076782,"base_score":2.70805020110221,"endowment":2.70805020110221,"self_citation_contribution":0.40620753016533157,"citation_network_contribution":0.15911050884234657,"self_endowment_contribution":0.40620753016533157,"citer_contribution":0.15911050884234657,"corpus_percentile":52.48169243287225,"corpus_rank":585,"citation_count":18,"citer_count":16,"citers_with_citation_signal":9,"citers_with_endowment":9,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9492,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-11-17","fair_score":46.6667,"fair_percentile":43.733509234828496,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":2443,"name":"Jin Li","orcid":"0000-0001-9339-3349","position":1,"is_corresponding":false},{"id":6308,"name":"Jun Wang","orcid":"0000-0003-2509-9599","position":2,"is_corresponding":false},{"id":19473,"name":"Ignacio Ibarra","orcid":"0000-0002-0371-3976","position":3,"is_corresponding":false},{"id":92272,"name":"Xuesen Cheng","orcid":"0000-0002-0678-4411","position":4,"is_corresponding":false},{"id":3578,"name":"Malte D. Luecken","orcid":"0000-0001-7464-7921","position":5,"is_corresponding":false},{"id":92273,"name":"Jiaxiong Liu","orcid":null,"position":6,"is_corresponding":false},{"id":92274,"name":"Aboozar Monavarfeshani","orcid":"0000-0001-8906-5115","position":7,"is_corresponding":false},{"id":33173,"name":"Wenjun Yan","orcid":"0000-0003-3568-4265","position":8,"is_corresponding":false},{"id":92275,"name":"Yiqiao Zheng","orcid":"0000-0003-4133-0439","position":9,"is_corresponding":false},{"id":92276,"name":"Zhen Zuo","orcid":"0000-0003-1555-1756","position":10,"is_corresponding":false},{"id":92277,"name":"Samantha Colborn","orcid":null,"position":11,"is_corresponding":false},{"id":92278,"name":"Berenice Cortez","orcid":null,"position":12,"is_corresponding":false},{"id":92279,"name":"Leah A. Owen","orcid":"0000-0003-3802-3868","position":13,"is_corresponding":false},{"id":20632,"name":"Karthik Shekhar","orcid":"0000-0003-4349-6600","position":15,"is_corresponding":false},{"id":20637,"name":"Joshua R. Sanes","orcid":"0000-0001-8926-8836","position":16,"is_corresponding":false},{"id":92281,"name":"Tim Stout","orcid":null,"position":17,"is_corresponding":false},{"id":92282,"name":"Shiming Chen","orcid":"0000-0002-9299-5767","position":18,"is_corresponding":false},{"id":92283,"name":"Yumei Li","orcid":"0000-0002-4908-8459","position":19,"is_corresponding":false},{"id":42,"name":"Fabian Joachim Theis","orcid":"0000-0002-2419-1943","position":21,"is_corresponding":false},{"id":92285,"name":"Samantha Lynn Zayas Colborn","orcid":null,"position":22,"is_corresponding":false},{"id":92286,"name":"Berenice Sarahi Cortez","orcid":null,"position":23,"is_corresponding":false},{"id":40849,"name":"Nicholas M. Tran","orcid":"0000-0002-4213-3499","position":24,"is_corresponding":false},{"id":54660,"name":"Margaret M. DeAngelis","orcid":"0000-0003-3731-142X","position":25,"is_corresponding":false},{"id":6713,"name":"Rui Chen","orcid":"0000-0002-4227-7732","position":0,"is_corresponding":true}],"reference_count":109,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"38014002","pmcid":"PMC10680922","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"green","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":52.5,"fair_a":67.5,"fair_i":25.0,"fair_r":41.6667,"fair_zscore":0.1316,"fair_rationale":{"fair_score":46.67,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":52.5,"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 (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no OpenAlex id","rationale":null},{"key":"f_metadata_richness","label":"Rich, machine-readable metadata","kind":"llm","weight":1.0,"fraction":0.25,"signal":null,"rationale":"The paper provides basic dataset descriptions (e.g., cell types, donor numbers) but lacks machine-readable metadata such as structured JSON-LD, formal metadata schemas, or persistent identifiers for the data beyond URLs."}]},"A":{"name":"Accessible","score":67.5,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":1.0,"signal":"Open Access","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"0 OA location(s)","rationale":null},{"key":"a_access_protocol","label":"Clear data/code access protocol","kind":"llm","weight":1.0,"fraction":0.75,"signal":null,"rationale":"The data and code are accessible via multiple platforms (CELLxGENE, UCSC, GitHub) with explicit URLs, but the access protocol is not fully standardized (e.g., no formal API documentation or authentication details for all resources)."}]},"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":"Standard single-cell formats (e.g., h5ad, mtx) are implied, but the paper does not explicitly state use of standard vocabularies (e.g., Cell Ontology for all clusters) or formal identifiers beyond gene symbols."}]},"R":{"name":"Reusable","score":41.67,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":1.0,"signal":"is_dataset","rationale":null},{"key":"r_reusability","label":"Data-availability statement, license & reproducibility","kind":"llm","weight":2.0,"fraction":0.667,"signal":null,"rationale":"A data-availability statement and a Creative Commons license are provided, and reproducibility is supported with code repositories, but the license is not machine-readable in the paper and some methodological details (e.g., exact software versions) are missing."}]}},"suggestions":["Add structured machine-readable metadata (e.g., JSON-LD) with persistent identifiers (e.g., DOIs for datasets).","Provide explicit, version-controlled data access APIs and authentication details in the paper.","State explicit use of community standard vocabularies (e.g., Cell Ontology terms) for all cell-type annotations.","Include a machine-readable license (e.g., embedded in metadata) and ensure all software versions are listed in the methods.","Document all file formats and provide a README with exact reproducibility steps in the GitHub repos."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-06-18T00:48:21.503493Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}