{"doi":"10.1073/pnas.1507125112","title":"A survey of human brain transcriptome diversity at the single cell level","abstract":"The human brain is a tissue of vast complexity in terms of the cell types it comprises. Conventional approaches to classifying cell types in the human brain at single cell resolution have been limited to exploring relatively few markers and therefore have provided a limited molecular characterization of any given cell type. We used single cell RNA sequencing on 466 cells to capture the cellular complexity of the adult and fetal human brain at a whole transcriptome level. Healthy adult temporal lobe tissue was obtained during surgical procedures where otherwise normal tissue was removed to gain access to deeper hippocampal pathology in patients with medical refractory seizures. We were able to classify individual cells into all of the major neuronal, glial, and vascular cell types in the brain. We were able to divide neurons into individual communities and show that these communities preserve the categorization of interneuron subtypes that is typically observed with the use of classic interneuron markers. We then used single cell RNA sequencing on fetal human cortical neurons to identify genes that are differentially expressed between fetal and adult neurons and those genes that display an expression gradient that reflects the transition between replicating and quiescent fetal neuronal populations. Finally, we observed the expression of major histocompatibility complex type I genes in a subset of adult neurons, but not fetal neurons. The work presented here demonstrates the applicability of single cell RNA sequencing on the study of the adult human brain and constitutes a first step toward a comprehensive cellular atlas of the human brain.","journal":"Proceedings of the National Academy of Sciences","year":2015,"id":8174,"datarank":14.929680986333308,"base_score":7.315218389752975,"endowment":7.315218389752975,"self_citation_contribution":1.0972827584629463,"citation_network_contribution":13.832398227870362,"self_endowment_contribution":1.0972827584629463,"citer_contribution":13.832398227870362,"corpus_percentile":87.30675345809601,"corpus_rank":157,"citation_count":1558,"citer_count":183,"citers_with_citation_signal":183,"citers_with_endowment":183,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.721,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2015-05-18","fair_score":33.8333,"fair_percentile":16.13896218117854,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":72350,"name":"Steven A. Sloan","orcid":"0000-0001-7769-7684","position":1,"is_corresponding":false},{"id":340,"name":"Ye Zhang","orcid":"0009-0000-4883-8097","position":2,"is_corresponding":false},{"id":72351,"name":"Martin Enge","orcid":"0000-0001-8748-8931","position":3,"is_corresponding":false},{"id":72352,"name":"Christine Caneda","orcid":null,"position":4,"is_corresponding":false},{"id":72353,"name":"Lawrence M. Shuer","orcid":"0000-0001-8121-223X","position":5,"is_corresponding":false},{"id":72354,"name":"Melanie G. Hayden Gephart","orcid":null,"position":6,"is_corresponding":false},{"id":68268,"name":"Ben A. Barres","orcid":"0000-0003-2905-4136","position":7,"is_corresponding":false},{"id":11049,"name":"Stephen R. Quake","orcid":"0000-0002-1613-0809","position":8,"is_corresponding":false},{"id":72355,"name":"Melanie Hayden Gephart","orcid":"0000-0003-2965-9231","position":9,"is_corresponding":false},{"id":72349,"name":"Spyros Darmanis","orcid":"0000-0003-4002-8158","position":0,"is_corresponding":true}],"reference_count":28,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"26060301","pmcid":"PMC4466750","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":69.0,"fair_a":48.0,"fair_i":5.0,"fair_r":13.3333,"fair_zscore":-1.0292,"fair_rationale":{"fair_score":33.83,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":69.0,"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 (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 does not mention any machine-readable metadata or structured descriptions of the data."}]},"A":{"name":"Accessible","score":48.0,"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":0.0,"signal":null,"rationale":"No protocol for accessing the data or code is provided; the text only describes the study without any access information."}]},"I":{"name":"Interoperable","score":5.0,"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":0.25,"signal":null,"rationale":"The paper uses standard terms like 'single cell RNA sequencing' but does not specify use of standard formats, vocabularies, or persistent identifiers."}]},"R":{"name":"Reusable","score":13.33,"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":0.0,"signal":null,"rationale":"No data-availability statement, license, or reproducibility details are given; the text only describes the study's findings."}]}},"suggestions":["Deposit the raw and processed single-cell RNA-seq data in a public repository (e.g., GEO or ArrayExpress) with a persistent identifier and include the accession number in the paper.","Provide a clear data-access protocol, such as a link to a repository or a statement on how to request data from the authors.","Use standard file formats (e.g., FASTQ, BAM, or HDF5) and controlled vocabularies (e.g., Cell Ontology terms) for cell types, and include a data dictionary.","Include a data-availability statement with a license (e.g., CC0 or CC-BY) and describe steps for reproducibility, such as providing the analysis code and software versions."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"abstract_only"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"abstract_only","fair_has_llm":true,"fair_computed_at":"2026-06-18T00:30:51.433934Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}