Single-cell genomics and regulatory networks for 388 human brains is a dataset published in Science (2024). On theSindex it has a DataRank of 1.7, placing it in the top 12.3% of the data-sharing corpus. It has been cited 155 times, with 100 citing works in its 1-hop citation network. Its calibrated FAIR score is 67/100.
Ranks in the top 12% for downstream scientific impact
Linked data & code
DataRank reads this dataset's downstream impact straight off the citation graph — no black box, no proprietary weighting. How is this computed?
FAIR checklist signals are shown for context only and do not affect DataRank scoring.
Full FAIR picture · advisory
The headline score is computed from the scored criteria — the fact-shaped checks (a repository, an accession, a licence) that two independent models agree on. The advisory criteria below are real FAIR guidance but rest on judgment calls that models read differently, so they inform without moving the number.
“Girgenti-snMultiome datasets are deposited at NCBI GEO (GSE261983) (110).”
The paper provides a GEO accession (GSE261983), which is a persistent identifier scheme. [majority verdict 'yes' (4/5 passes agreed)]
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'
“Girgenti-snMultiome datasets are deposited at NCBI GEO (GSE261983) (110).”
NCBI GEO is a recognised data repository. [majority verdict 'yes' (4/5 passes agreed)]
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
“Girgenti-snMultiome datasets are deposited at NCBI GEO (GSE261983) (110).”
The dataset identifier GSE261983 appears only in the body text, not in the reference list. [majority verdict 'partial' (4/5 passes agreed)]
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'
Advisory · not in the published score
“Girgenti-snMultiome datasets are deposited at NCBI GEO (GSE261983) (110).”
The data-availability statement points to a repository record (NCBI GEO) with an accession, meeting Colavizza category 3. [majority verdict 'yes' (4/5 passes agreed)]
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
“The resource can be summarized at multiple levels: (1) raw data and metadata with a harmonized identifier system for each of the individuals; (2) quantifications of single-cell gene expression (count matrices) with a BICCN-compatible cell-typing system for the PFC; (3) lists of DE genes and differential cell-fractions for various phenotypes; (4) snATAC-seq signal tracks for various cell types and ENCODE-compatible regulatory elements (b-cCREs and scCREs), including lists of validated ones; (5) the variability for each gene and functional category (by individual, cell type, and brain region) and the associated sequence conservation of genes and regulatory elements; (6) a core set of GTEx-compatible scQTLs and other additional sets of QTLs (such as dynamic eQTLs); (7) full GRNs for each cell type, including enhancer-to-gene and TF-to-regulatory element links, and associated files relating each downstream gene to its most significant upstream regulators; (8) cell-to-cell communication networks (expressed as ligand-receptor- by-cell-type matrices); (9) integrative models with code for imputation, perturbation and prioritization of cell-type-specific functional genomics in brain disease; and (10) the resulting prioritized genes, cell types, and cell-to-cell linkages.”— not found in the paper; verdict downgraded
The paper provides an itemised inventory of the dataset components in the Discussion section. [downgraded to 'partial' — no verifiable quote from the paper]
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'
“All sequencing data, derived analysis files, and computer codes are available from the brainSCOPE resource portal (brainscope.psychencode.org, figs. S3–S5; (20))”
The paper states that the data are available from the brainSCOPE portal without any stated precondition, and the Girgenti-snMultiome data at GEO are also openly accessible.
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'
Advisory · not in the published score
“All sequencing data, derived analysis files, and computer codes are available from the brainSCOPE resource portal (brainscope.psychencode.org, figs. S3–S5; (20))”
The paper describes the action of accessing the data through the portal but does not apply an explicit access-level label (e.g., 'open access'). [majority verdict 'partial' (2/5 passes agreed)]
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
“Raw datasets for the PsychENCODE cohorts, as well as protected-access integrated datasets such as imputed genotypes, are available at the PsychENCODE Knowledge portal (108).”
The paper names an institutional gatekeeper (the PsychENCODE Knowledge portal) for the sensitive human-subject data, consistent with controlled-access procedures. [majority verdict 'yes' (4/5 passes agreed)]
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
No persistence commitment or availability timing is stated for the study's data. [majority verdict 'no' (4/5 passes agreed)]
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'
No file format is named for the released data in the main text.
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
Advisory · not in the published score
“BICCN-compatible cell-typing system”
The paper names BICCN, a community standard for cell typing. [majority verdict 'yes' (4/5 passes agreed)]
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'
No identifier for an external resource (e.g., accession, DOI) is given in the text; only references to publications are provided. [majority verdict 'no' (3/5 passes agreed)]
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'
No licence is named for the data.
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'
No version token or date is given for the data snapshot.
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'
“Code used in this manuscript is deposited on GitHub and linked from the brainSCOPE portal (112).”
The paper states that code is deposited on GitHub, a machine-resolvable code repository. [majority verdict 'yes' (4/5 passes agreed)]
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)
“U01DA048279”
The paper lists multiple grant numbers, including U01DA048279.
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
Advisory · not in the published score
The main text does not name specific instruments, kits, or software versions used to produce the data. [majority verdict 'no' (3/5 passes agreed)]
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
No documentation object (README, codebook) is stated to accompany the data. [majority verdict 'no' (4/5 passes agreed)]
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
Calibrated FAIR score — a parallel quality metric, independent of the DataRank citation score. See the full evaluation →
Base Score Contribution
0.757
From this paper's citation signal
Citation Network Contribution
0.945
From 58 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 100 citers.
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NIDA NIH HHS
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NICHD NIH HHS
Grant: P50 HD105353
NIA NIH HHS
Grant: R01 AG065582
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National Institutes of Health
Grant: 1U01MH122678-01
1/2 Identification and Validation of Expression Quantitative Trait Loci (eQTLs) in discrete cell types across human brain development
National Institutes of Health
Grant: 5U01MH116438-04
Massively parallel characterization of psychiatric disease associated regulatory elements in defined cell types
National Institutes of Health
Grant: 5U01MH103339-02
Transcriptional and Epigenetic Signatures of Human Brain Development and Autism
National Institutes of Health
Grant: 5R01MH126459-04
Gene Expression Regulation in Brains of East Asian, African, and European Descent Explains Schizophrenia GWAS Across Populations
National Institutes of Health
Grant: 5U01MH103392-03
Cis-Regulatory Epigenome Mappings in Schizophrenia
National Institutes of Health
Grant: 1U01MH122509-01
Discovery and validation of genetic variation impacting the gene regulatory landscape during human cortical development
National Institutes of Health
Grant: 3U01MH103365-03S1
Gene regulatory elements and transcriptome in iPSCs and embryonic human cortex
National Institutes of Health
Grant: 5U01MH116442-03
The 3D genome in transcriptional regulation across the postnatal life span, with implications for schizophrenia and bipolar disorder
National Institutes of Health
Grant: 5R01MH109677-02
Risk genetic variants and cis regulation of gene expression in Bipolar Disorder
National Institutes of Health
Grant: 3U01DA048279-03S1
Functional genomic resource and integrative model of dopaminergic circuitry associated with psychiatric disease
National Institutes of Health
Grant: 5R01MH094714-02
Epigenetic and Transcriptional Dysregulation in Autism Spectrum Disorder
National Institutes of Health
Grant: 5U01MH122849-02
Spatial registration of gene expression in the human brain
National Institutes of Health
Grant: 5R01MH117293-03
1/3 Understanding PTSD through Postmortem Targeted Brain Multi-omics
National Institutes of Health
Grant: 5P50MH106934-04
Functional Genomics of Human Brain Development
National Institutes of Health
Grant: 5R01MH110905-04
2/2-Measuring translational dynamics and the proteome to identify potential brain biomarkers for psychiatric disease
National Institutes of Health
Grant: 5R01MH110926-04
1/3 Integrative Genomic Analysis of Human Brain Development and Autism
National Institutes of Health
Grant: 1R01MH109715-01A1
Mapping the role of long noncoding RNAs in gene regulatory networks in schizophrenia
National Institutes of Health
Grant: 1RF1MH128970-01
A regulome and transcriptome atlas of fetal and adult human neurogenesis
National Institutes of Health
Grant: 5R01MH110927-02
2/3 Integrative Genomic Analysis of Human Brain Development and Autism
National Institutes of Health
Grant: 5R21MH109956-02
Characterizing the developing human brain transcriptome at single-base resolution
National Institutes of Health
Grant: 5R01MH116529-05
Integrated, cell type specific functional genomics analyses of regulatory sequence elements and their dynamic interaction networks in neuropsychiatric brain tissues
National Institutes of Health
Grant: 5R21MH103877-02
GABA Epigenomes in Autism
National Institutes of Health
Grant: 5R21MH105881-02
Long non-coding RNAs in gene regulatory networks underlying Autism
National Science Foundation
Grant: 2144475
CAREER: Interpretable machine learning deciphers single-cell multi-modal data for understanding cell-type functional genomics in complex brains
National Institutes of Health
Grant: 5R21NS127432-02
Creation of a Schwann Cell Gene Regulatory Network
National Institutes of Health
Grant: 5R21MH105853-02
Decomposing cell type-specific marks in post-mortem human brain studies
National Institutes of Health
Grant: 5R01AG065582-04
Understanding the protective and neuroinflammatory role of human brain immune cells in Alzheimer Disease
National Institutes of Health
Grant: 5R01MH117406-03
The Spatiotemporal Landscape of the Human Brain Epitranscriptome
National Institutes of Health
Grant: 5U01MH122681-02
2/2 - Identification and Validation of Expression Quantitative Trait Loci (eQTLs) in discrete cell types across human brain development
National Institutes of Health
Grant: 1R01MH125516-01A1
Assessing Genomic, Regulatory and Transcriptional Variation at Single Nuclei Resolution in the Brains of Individuals with Autism Spectrum Disorder
National Institutes of Health
Grant: 1R01NS128523-01
Interpretable Deep Learning Methods to Investigate Genetics and Epigenetics of Alzheimer's Disease at a Single-Cell Resolution
National Institutes of Health
Grant: 1R56MH114911-01A1
1/3 Chromatin regulation during brain development and in ASD
National Institutes of Health
Grant: 1R21NS128761-01
Prediction and Validation of Oligodendrocyte Gene Regulatory Network from Multi-Omics
National Institutes of Health
Grant: 5R01MH121521-03
Isoform-level probabilistic transcriptome-wide association to undercover neurogenetic mechanisms underlying complex psychiatric traits
National Institutes of Health
Grant: 5R01MH125246-05
Multiethnic genomic epigenomic and transcriptomic fine-mapping and functional validation analysis of schizophrenia and bipolar disorder risk loci
National Institutes of Health
Grant: 1R01MH126393-01
Laminar dissection of cortical human brain gene expression in neuropsychiatric disorders
National Institutes of Health
Grant: 5U01MH114812-04
A multimodal atlas of human brain cell types
National Institutes of Health
Grant: 1R56MH114901-01A1
3/3 Chromatin regulation during brain development and in ASD
National Institutes of Health
Grant: 5R01MH111721-04
Integrative Genomics of the Corticolimbic Circuit in Major Depressive Disorder
National Institutes of Health
Grant: 1P50HD105353-01
Waisman Center Intellectual and Developmental Disabilities Research Center
National Institutes of Health
Grant: 5U01MH116492-02
1/2 Discovery and validation of neuronal enhancers associated with the development of psychiatric disorders
National Institutes of Health
Grant: 1U01MH116441-01
Dynamic RNA Modifications in human brain development and autism
National Institutes of Health
Grant: 5R01HG012572-02
Decoding the Noncoding Regulatory Genome with Super-resolution via Single-cell Multiomics Integration
National Institutes of Health
Grant: 1R01MH110928-01
3/3 Integrative Genomic Analysis of Human Brain Development and Autism
National Institutes of Health
Grant: 5U01MH122590-02
2/3 High-resolution mapping of cell type-specific DNA (hydroxy)methylation in the human brain during postnatal development and in psychiatric disease
National Institutes of Health
Grant: 3U01MH103340-02S1
Genetic variants affect brain gene expression and risks of psychiatric disorders
National Institutes of Health
Grant: 1RF1MH128695-01A1
Machine learning analyses of single-cell multi-modal data for understanding cell-type functional genomics and gene regulation
National Institutes of Health
Grant: 5R01MH110921-04
Molecular Profiling of Schizophrenia
National Institutes of Health
Grant: 3R01AG050986-04S1
Higher Order Chromatin and Genetic Risk for Alzheimer's Disease
National Institutes of Health
Grant: 5R01AG067025-04
Understanding the molecular mechanisms that contribute to neuropsychiatric symptoms in Alzheimer Disease
National Institutes of Health
Grant: 5R01MH105472-03
Decoding schizophrenia-From GWAS to functional regulatory variants
National Institutes of Health
Grant: 1R01MH117291-01
2/3 Understanding PTSD through Postmortem Targeted Brain Multi-omics
National Institutes of Health
Grant: 1R01MH109897-01
Integrated Multiscale Networks in Schizophrenia
National Institutes of Health
Grant: 5U01MH116487-02
2/2 - Cell Type and Region-Specific Regulatory Networks in Human Brain Development and Disorders
National Institutes of Health
Grant: 5U01MH116489-06
2/2 Discovery and validation of neuronal enhancers associated with the development of psychiatric disorders
National Institutes of Health
Grant: 5U01MH116488-03
1/2 Cell Type and Region-Specific Regulatory Networks in Human Brain Development and Disorders
National Institutes of Health
Grant: 5U01MH122592-03
3/3 High-resolution mapping of cell type-specific DNA (hydroxy)methylation in the human brain during postnatal development and in psychiatric disease
National Institutes of Health
Grant: 5R01MH117292-03
Site 3/3, Understanding PTSD through Postmortem Targeted Brain Multiomics
National Institutes of Health
Grant: 5U01MH103346-02
The USC PsychENCODE Project
National Institutes of Health
Grant: 1R01MH123922-01
Population-level and mechanistic dissection of 17q21 structural variant association with psychiatric traits
National Institutes of Health
Grant: 1R21MH102791-01A1
Establishing comprehensive and quantitative maps of DNA methylation in the develo
National Institutes of Health
Grant: 5R01MH105898-04
RNA Sequencing of the Limbic System in Bipolar Disorder
National Institutes of Health
Grant: 5U19AG060909-02
A platform for cell type-level transcriptomic, epigenomic and spatial interrogation of Alzheimer's disease
National Institutes of Health
Grant: 5U01MH122591-03
1/3 High-resolution mapping of cell type-specific DNA (hydroxy)methylation in the human brain during postnatal development and in psychiatric disease.
National Institutes of Health
Grant: 1R56MH114899-01A1
2/3 Chromatin regulation during brain development and in ASD
National Institutes of Health
Grant: 5R01MH110920-04
1/2 Measuring translational dynamics and the proteome to identify potential brain biomakers for psychiatric disease
National Institutes of Health
Grant: 5R01MH129301-03
Sex-specific trajectories in epigenomic regulation of brain patterning
Fields of Study
MeSH Terms
Keywords
Sustainable Development Goals