{"doi":"10.1126/science.adf5357","title":"Single-cell DNA methylation and 3D genome architecture in the human brain","abstract":"Delineating the gene-regulatory programs underlying complex cell types is fundamental for understanding brain function in health and disease. Here, we comprehensively examined human brain cell epigenomes by probing DNA methylation and chromatin conformation at single-cell resolution in 517 thousand cells (399 thousand neurons and 118 thousand non-neurons) from 46 regions of three adult male brains. We identified 188 cell types and characterized their molecular signatures. Integrative analyses revealed concordant changes in DNA methylation, chromatin accessibility, chromatin organization, and gene expression across cell types, cortical areas, and basal ganglia structures. We further developed single-cell methylation barcodes that reliably predict brain cell types using the methylation status of select genomic sites. This multimodal epigenomic brain cell atlas provides new insights into the complexity of cell-type-specific gene regulation in adult human brains.","journal":"Science","year":2023,"id":315467,"datarank":3.097248580438234,"base_score":5.0689042022202315,"endowment":5.0689042022202315,"self_citation_contribution":0.7603356303330349,"citation_network_contribution":2.3369129501051993,"self_endowment_contribution":0.7603356303330349,"citer_contribution":2.3369129501051993,"corpus_percentile":92.8366983832289,"corpus_rank":927,"citation_count":158,"citer_count":100,"citers_with_citation_signal":89,"citers_with_endowment":89,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.7806,"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":62.5,"fair_percentile":81.0149801284011,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":37793,"name":"Jingtian Zhou","orcid":"0000-0003-2060-1922","position":1,"is_corresponding":false},{"id":37782,"name":"Anna Bartlett","orcid":"0000-0001-7059-4033","position":2,"is_corresponding":false},{"id":218491,"name":"Qiurui Zeng","orcid":"0000-0002-2252-7669","position":3,"is_corresponding":false},{"id":553409,"name":"Hanqing Liu","orcid":"0000-0002-5114-6048","position":4,"is_corresponding":false},{"id":37784,"name":"Rosa G. Castanon","orcid":"0000-0003-1791-002X","position":5,"is_corresponding":false},{"id":985473,"name":"Mia Kenworthy","orcid":"0000-0003-1704-6817","position":6,"is_corresponding":false},{"id":985474,"name":"Jordan Altshul","orcid":"0000-0001-5999-3295","position":7,"is_corresponding":false},{"id":985475,"name":"Cynthia Valadon","orcid":"0000-0003-1655-6903","position":8,"is_corresponding":false},{"id":38325,"name":"Andrew I. Aldridge","orcid":"0000-0003-1962-8802","position":9,"is_corresponding":false},{"id":3788,"name":"Joseph R. Nery","orcid":"0000-0003-0153-5659","position":10,"is_corresponding":false},{"id":37795,"name":"Huaming Chen","orcid":"0000-0001-5289-7882","position":11,"is_corresponding":false},{"id":985476,"name":"Jiaying Xu","orcid":"0009-0004-1919-1465","position":12,"is_corresponding":false},{"id":774953,"name":"Nicholas D. Johnson","orcid":"0000-0003-3229-6849","position":13,"is_corresponding":false},{"id":38391,"name":"Jacinta D. Lucero","orcid":"0000-0001-7578-6624","position":14,"is_corresponding":false},{"id":38352,"name":"Julia K. Osteen","orcid":"0000-0001-7058-3297","position":15,"is_corresponding":false},{"id":985477,"name":"Nora Emerson","orcid":"0000-0001-7344-4487","position":16,"is_corresponding":false},{"id":985478,"name":"Jon Rink","orcid":"0009-0007-4651-0443","position":17,"is_corresponding":false},{"id":985479,"name":"Jasper Lee","orcid":"0000-0003-2086-1441","position":18,"is_corresponding":false},{"id":38344,"name":"Yang Eric Li","orcid":"0000-0001-6997-6018","position":19,"is_corresponding":false},{"id":38363,"name":"Kimberly Siletti","orcid":"0000-0001-7620-8973","position":20,"is_corresponding":false},{"id":985480,"name":"Michelle Liem","orcid":"0009-0004-0542-7166","position":21,"is_corresponding":false},{"id":986031,"name":"Naomi Claffey","orcid":null,"position":22,"is_corresponding":false},{"id":58970,"name":"Carolyn O’Connor","orcid":"0000-0002-3301-7912","position":23,"is_corresponding":false},{"id":38371,"name":"Anna Marie Yanny","orcid":"0000-0001-7250-8450","position":24,"is_corresponding":false},{"id":551983,"name":"Julie Nyhus","orcid":"0000-0002-2006-8235","position":25,"is_corresponding":false},{"id":38332,"name":"Nick Dee","orcid":"0000-0002-2831-9254","position":26,"is_corresponding":false},{"id":38327,"name":"Tamara Casper","orcid":"0000-0003-1638-3651","position":27,"is_corresponding":false},{"id":550264,"name":"Nadiya V. Shapovalova","orcid":"0000-0002-8618-8272","position":28,"is_corresponding":false},{"id":550260,"name":"Daniel Hirschstein","orcid":"0009-0001-5839-6023","position":29,"is_corresponding":false},{"id":38390,"name":"Song‐Lin Ding","orcid":"0000-0002-7072-5272","position":30,"is_corresponding":false},{"id":38321,"name":"Rebecca D. Hodge","orcid":"0000-0002-5784-9668","position":31,"is_corresponding":false},{"id":550261,"name":"Boaz P. Levi","orcid":"0000-0002-8346-872X","position":32,"is_corresponding":false},{"id":38380,"name":"C. Dirk Keene","orcid":"0000-0002-5291-1469","position":33,"is_corresponding":false},{"id":38388,"name":"Sten Linnarsson","orcid":"0000-0002-3491-3444","position":34,"is_corresponding":false},{"id":38389,"name":"Ed S. Lein","orcid":"0000-0001-9012-6552","position":35,"is_corresponding":false},{"id":136223,"name":"Bing Ren","orcid":"0000-0002-5435-1127","position":36,"is_corresponding":false},{"id":38373,"name":"M. Margarita Behrens","orcid":"0000-0002-7168-8186","position":37,"is_corresponding":false},{"id":3799,"name":"Joseph R. Ecker","orcid":"0000-0001-5799-5895","position":38,"is_corresponding":false},{"id":618852,"name":"Wei Tian","orcid":"0000-0002-2146-1717","position":0,"is_corresponding":true}],"reference_count":100,"raw_metadata":null,"created_at":"2026-07-19T01:06:25.560098Z","pmid":"37824674","pmcid":"PMC10572106","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":72.2222,"fair_a":50.0,"fair_i":20.0,"fair_r":25.0,"fair_zscore":1.1103,"fair_rationale":{"fair_score":62.5,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":72.22,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Raw and processed data were also deposited to NCBI GEO/SRA with accession number GSE215353.","grounded":true,"rationale":"The paper provides a repository accession (GSE215353) that is a persistent identifier in a registered scheme.","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Raw and processed data were also deposited to NCBI GEO/SRA with accession number GSE215353.","grounded":true,"rationale":"NCBI GEO/SRA is a named data repository. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"The data analyzed in this study were produced through the Brain Initiative Cell Census Network (BICCN:RRID:SCR_015820) and deposited in the NEMO Archive (RRID:SCR_002001) under identifier nemo:dat-jx4eu3g accessible at https://assets.nemoarchive.org/dat-jx4eu3g. Raw and processed data were also deposited to NCBI GEO/SRA with accession number GSE215353.","grounded":false,"rationale":"The statement points at a repository record with an accession number and a persistent link. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","anchors":["Colavizza, Hrynaszkiewicz, Staden, Whitaker & McGillivray (2020), 'The citation advantage of li","Springer Nature research data policy — Data Availability Statements: standard statement templat","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes"],"scored":false,"signal":null},{"key":"f_discovery_metadata","label":"Description of the dataset as an object","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"We comprehensively examine human brain cell epigenomes by probing DNA methylation and chromatin conformation at single-cell resolution in 517k cells (399k neurons and 118k non-neurons) from 46 regions of three adult male brains.","grounded":true,"rationale":"The paper describes the dataset's content and size in a running prose sentence, not an itemized inventory. [majority verdict 'partial' (4/5 passes agreed)]","anchors":["RDA-F2-01M — 'Rich metadata is provided to allow discovery' (priority Essential)","FsF-F2-01M — F-UJI: 'Metadata includes descriptive core elements to support data findability'","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'"],"scored":false,"signal":null},{"key":"f_dataset_cited","label":"Dataset formally cited","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"Raw and processed data were also deposited to NCBI GEO/SRA with accession number GSE215353.","grounded":true,"rationale":"The dataset's identifier appears only in the body text, not as a reference-list entry.","anchors":["FORCE11 Joint Declaration of Data Citation Principles (2014) — data should be cited as a first-","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes","FsF-F3-01M — F-UJI: 'Metadata includes the identifier of the data it describes'"],"scored":true,"signal":null}]},"A":{"name":"Accessible","score":50.0,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Raw and processed data were also deposited to NCBI GEO/SRA with accession number GSE215353.","grounded":true,"rationale":"The text gives a route to the data with no stated precondition. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-A1.1-01D — 'Data is accessible through a free access protocol'","FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":"accessible at https://assets.nemoarchive.org/dat-jx4eu3g","grounded":false,"rationale":"The paper describes an action (accessible at a URL) but does not label the access level with a standard term. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","anchors":["FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","RDA-A1-01M — metadata contains information to enable the user to get access to the data","COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The data are openly deposited with no gatekeeper named; the paper does not indicate controlled access.","anchors":["NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee","RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and ","NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No sentence states when the data are available or how long they persist.","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":20.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No file-format token is named for the released data.","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No data or metadata community standard is named for the dataset.","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"The data analyzed in this study were produced through the Brain Initiative Cell Census Network (BICCN:RRID:SCR_015820) and deposited in the NEMO Archive (RRID:SCR_002001)","grounded":true,"rationale":"The paper gives RRIDs for the consortium and the archive, which are identifiers for resources other than the dataset. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":25.0,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No licence artefact is named for the data; the paper's CC-BY licence applies to the article, not the data.","anchors":["RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu","RDA-R1.1-02M — 'Metadata refers to a standard reuse licence'","RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"snmC-seq3","grounded":false,"rationale":"The paper names the specific assay technology used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","anchors":["RDA-R1.2-01M — 'Metadata includes provenance information according to community- specific standa","FsF-R1.2-01M — F-UJI: 'Metadata includes provenance information about data creation or generati","W3C PROV-O (W3C Recommendation, 2013) — the entity/activity/agent model of provenance"],"scored":false,"signal":null},{"key":"r_documentation_codebook","label":"Documentation / codebook","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not mention a README, data dictionary, or codebook that accompanies the deposited data. [majority verdict 'no' (4/5 passes agreed)]","anchors":["RDA-R1-01M — '(Meta)data are richly described with a plurality of accurate and relevant attribu","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'","NIH DMS Policy Element 3 (NOT-OD-21-014) — Standards (documentation and metadata to accompany t"],"scored":false,"signal":null},{"key":"r_versioning","label":"Snapshot identified","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"Neither a version token nor a date is provided to pin the data snapshot.","anchors":["DataCite Metadata Schema 4.6 — the 'Version' property","RDA-R1.2-01M — provenance information (which version was used is provenance)","NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"https://github.com/jksr/human-brain-atlas-code","grounded":false,"rationale":"The paper provides a machine-resolvable URL to a code repository for the analysis code. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","anchors":["NIH DMS Policy Element 2 (NOT-OD-21-014) — 'Related Tools, Software and/or Code'","FAIR4RS Principles v1.0 (Chue Hong et al., 2022; RDA/FORCE11/ReSA) — FAIR Principles for Resear","FORCE11 Software Citation Principles (Smith, Katz & Niemeyer, 2016, PeerJ CS 2:e86)"],"scored":true,"signal":null},{"key":"x_funding_attribution","label":"Funder and award number","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"This work was supported by grants from NIMH U01MH121282 to B.R., M.M.B and J.R.E.","grounded":true,"rationale":"An award/grant number is provided along with the funder name.","anchors":["DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award","Crossref Funder Registry — canonical funder identifiers for funding metadata","RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco"],"scored":true,"signal":null}]}},"actions":[{"key":"r_reuse_license","dimension":"R","label":"Reuse licence","action":"Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No licence artefact is named for the data; the paper's CC-BY licence applies to the article, not the data.","gain":16.67,"priority":"essential","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No file-format token is named for the released data.","gain":8.33,"priority":"important","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Raw and processed data were also deposited to NCBI GEO/SRA with accession number GSE215353.","why":"The dataset's identifier appears only in the body text, not as a reference-list entry.","gain":4.17,"priority":"important","scored":true},{"key":"x_code_availability","dimension":"R","label":"Analysis code available","action":"Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"https://github.com/jksr/human-brain-atlas-code","why":"The paper provides a machine-resolvable URL to a code repository for the analysis code. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"Neither a version token nor a date is provided to pin the data snapshot.","gain":4.17,"priority":"useful","scored":true},{"key":"f_data_availability_statement","dimension":"F","label":"Data-availability statement","action":"Replace the statement with the repository template: name the repository and give the accession or DOI (Colavizza category 3). This is the only DAS class associated with a measured citation advantage; 'available on reasonable request' and 'within the article' are not.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The data analyzed in this study were produced through the Brain Initiative Cell Census Network (BICCN:RRID:SCR_015820) and deposited in the NEMO Archive (RRID:SCR_002001) under identifier nemo:dat-jx4eu3g accessible at https://assets.nemoarchive.org/dat-jx4eu3g. Raw and processed data were also deposited to NCBI GEO/SRA with accession number GSE215353.","why":"The statement points at a repository record with an accession number and a persistent link. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"f_discovery_metadata","dimension":"F","label":"Description of the dataset as an object","action":"Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"We comprehensively examine human brain cell epigenomes by probing DNA methylation and chromatin conformation at single-cell resolution in 517k cells (399k neurons and 118k non-neurons) from 46 regions of three adult male brains.","why":"The paper describes the dataset's content and size in a running prose sentence, not an itemized inventory. [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"a_access_conditions_stated","dimension":"A","label":"Access level labelled","action":"State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. A reader — and a harvester — should not have to infer the access level from the presence of a download link.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"accessible at https://assets.nemoarchive.org/dat-jx4eu3g","why":"The paper describes an action (accessible at a URL) but does not label the access level with a standard term. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"i_community_standard_vocabulary","dimension":"I","label":"Community standard / vocabulary","action":"Adopt and NAME your domain's data standard — the minimum-information checklist, metadata schema, or ontology your community uses (MIAME/MINSEQE, ISA-Tab, BIDS, an OBO ontology, HL7 FHIR/OMOP) — and say which one you followed. A reporting checklist standardises your paper; it does nothing for your data. In genomics / sequencing, describe the data with MIAME, MINSEQE or MIxS.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No data or metadata community standard is named for the dataset.","gain":0.0,"priority":"important","scored":false},{"key":"r_provenance_methods","dimension":"R","label":"Provenance of the data","action":"Name the instruments, kits, and software — with versions — that produced the data, not just the verbs. 'Reads were aligned' is not provenance; 'aligned with STAR v2.7.9a to GRCh38' is, because someone else can rerun it.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"snmC-seq3","why":"The paper names the specific assay technology used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not mention a README, data dictionary, or codebook that accompanies the deposited data. [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data. For sensitive/human genomics / sequencing data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The data are openly deposited with no gatekeeper named; the paper does not indicate controlled access.","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No sentence states when the data are available or how long they persist.","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI).","Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"unpaywall_pdf"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"unpaywall_pdf","fair_has_llm":true,"fair_computed_at":"2026-07-20T10:57:50.593314Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}