{"doi":"10.1016/j.celrep.2025.116047","title":"A spatiotemporal atlas of mouse gastrulation and early organogenesis to explore axial patterning and project in vitro models onto in vivo space","abstract":"During gastrulation, mouse epiblast cells form the three germ layers that establish the body plan and initiate organogenesis. While single-cell atlases have advanced our understanding of lineage diversification, spatial aspects of differentiation remain poorly defined. Here, we applied spatial transcriptomics to mouse embryos at embryonic (E) E7.25 and E7.5 days and integrated these data with existing E8.5 spatial and E6.5-E9.5 single-cell RNA-seq atlases. This resulted in a spatiotemporal atlas of over 150,000 cells with 82 refined cell-type annotations. The resource enables exploration of gene expression dynamics across anterior-posterior and dorsal-ventral axes, uncovering spatial logic guiding mesodermal fate decisions in the primitive streak. We also developed a computational pipeline to project additional single-cell datasets into this framework for comparative analysis. Freely accessible through an interactive web portal, this atlas offers a valuable tool for the developmental and stem cell biology communities to investigate mouse embryogenesis in a spatial and temporal context.","journal":"Cell Reports","year":2025,"id":514421,"datarank":0.3952608247976616,"base_score":2.1972245773362196,"endowment":2.1972245773362196,"self_citation_contribution":0.32958368660043297,"citation_network_contribution":0.06567713819722863,"self_endowment_contribution":0.32958368660043297,"citer_contribution":0.06567713819722863,"corpus_percentile":53.7943838477605,"corpus_rank":5974,"citation_count":8,"citer_count":8,"citers_with_citation_signal":3,"citers_with_endowment":3,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.6919,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":58.3333,"fair_percentile":72.8829104249465,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":552846,"name":"Tim Lohoff","orcid":"0000-0001-9333-842X","position":1,"is_corresponding":false},{"id":552847,"name":"Noushin Koulena","orcid":"0000-0002-9419-5712","position":2,"is_corresponding":false},{"id":552848,"name":"Nico Pierson","orcid":"0000-0002-2451-0633","position":3,"is_corresponding":false},{"id":52907,"name":"Constantin Pape","orcid":"0000-0001-6562-7187","position":4,"is_corresponding":false},{"id":1377021,"name":"Farhan Ameen","orcid":"0009-0005-1690-1086","position":5,"is_corresponding":false},{"id":281577,"name":"Jonathan A. Griffiths","orcid":"0000-0002-2010-2296","position":6,"is_corresponding":false},{"id":1377022,"name":"Bart Theeuwes","orcid":"0000-0003-3089-4773","position":7,"is_corresponding":false},{"id":27,"name":"Nicola K. Wilson","orcid":"0000-0003-0865-7333","position":8,"is_corresponding":false},{"id":552518,"name":"Anna Kreshuk","orcid":"0000-0003-1334-6388","position":9,"is_corresponding":false},{"id":44527,"name":"Wolf Reik","orcid":"0000-0003-0216-9881","position":10,"is_corresponding":false},{"id":281579,"name":"Jennifer Nichols","orcid":"0000-0002-8650-1388","position":11,"is_corresponding":false},{"id":552853,"name":"Long Cai","orcid":"0000-0002-7154-5361","position":12,"is_corresponding":false},{"id":15932,"name":"John C. Marioni","orcid":"0000-0001-9092-0852","position":13,"is_corresponding":false},{"id":43,"name":"Berthold Göttgens","orcid":"0000-0001-6302-5705","position":14,"is_corresponding":false},{"id":80914,"name":"Shila Ghazanfar","orcid":"0000-0001-7861-6997","position":15,"is_corresponding":false},{"id":824272,"name":"Luke Harland","orcid":"0000-0002-2821-5893","position":0,"is_corresponding":true}],"reference_count":85,"raw_metadata":null,"created_at":"2026-07-19T02:48:29.165853Z","pmid":"40728928","pmcid":"PMC7618461","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":61.1111,"fair_a":62.5,"fair_i":0.0,"fair_r":50.0,"fair_zscore":0.9454,"fair_rationale":{"fair_score":58.33,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":61.11,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"DAPI images, molecules, and segmentation boundaries can be downloaded from Zenodo at https://zenodo.org/records/13977985 .","grounded":true,"rationale":"The only identifier for the dataset is a URL (https://zenodo.org/records/13977985), which is not a PID scheme string (DOI, Handle, ARK, URN, or repository accession) as defined in the rubric. [majority verdict 'partial' (3/5 passes agreed)]","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":"DAPI images, molecules, and segmentation boundaries can be downloaded from Zenodo at https://zenodo.org/records/13977985 .","grounded":true,"rationale":"Zenodo is a named data repository (registered in re3data/FAIRsharing) that holds the study's data. [majority verdict 'yes' (3/5 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":1.0,"verdict":"yes","evidence":"Data can be interactively explored at this link: http://shiny.maths.usyd.edu.au/SpatiotemporalMouseAtlas/ . Processed data can be downloaded using the links provided on the front page of the interactive exploration Shiny app above. DAPI images, molecules, and segmentation boundaries can be downloaded from Zenodo at https://zenodo.org/records/13977985 . All analyses were performed in R (version 4.2.1). Scripts for analysis and figure panels in this manuscript are available at https://github.com/ltgharland/Spatiotemporal-Atlas-of-Mouse-Gastrulation .","grounded":true,"rationale":"The data availability statement points to a repository record (Zenodo) with a persistent link, satisfying Colavizza category 3. [majority verdict 'yes' (3/5 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":0.0,"verdict":"no","evidence":"seqFISH on a total of 20 optical sagittal sections from four embryos (five optical sections/embryo) that were collected at E6.5 and E7.5 (Figures 1A–1E and S1A; Videos S1 and S2). After sample preparation, imaging, cell segmentation, and mRNA dot calling, we computed normalized gene expression levels for 351 genes across 14,794 cells (Figure 1E).","grounded":false,"rationale":"The dataset's content and extent are described in running prose (number of sections, embryos, genes, cells) but there is no itemised inventory such as a Data Records section or table listing files or variables. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 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":"DAPI images, molecules, and segmentation boundaries can be downloaded from Zenodo at https://zenodo.org/records/13977985 .","grounded":true,"rationale":"The dataset identifier (Zenodo URL) appears only in the body text of the Data Availability Statement and Key Resources Table, not as a reference-list entry. [majority verdict 'partial' (3/5 passes agreed)]","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":62.5,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"DAPI images, molecules, and segmentation boundaries can be downloaded from Zenodo at https://zenodo.org/records/13977985 .","grounded":true,"rationale":"The text gives a route to the data (Zenodo download) with no stated precondition such as embargo, registration, or request. [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":0.5,"verdict":"partial","evidence":"DAPI images, molecules, and segmentation boundaries can be downloaded from Zenodo at https://zenodo.org/records/13977985 .","grounded":true,"rationale":"The paper describes an action (download from Zenodo) without applying an explicit access-level label, so the access level must be inferred. [majority verdict 'partial' (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 from mouse embryos, not human subjects, so no gatekeeper is named; the paper does not address sensitive data 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":"The paper does not mention any temporal commitment: neither a retention period nor an availability timing.","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":0.0,"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 (open or proprietary) is named for the released data; the paper only describes the data as 'seqFISH images' and 'processed data' without specifying formats.","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 community data or metadata standard (e.g., MIAME, MIxS, BIDS, an ontology) is named as being applied to the data; only manuscript reporting guidelines may be present but not for the data.","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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper cites external resources (e.g., other atlases, software) but does not provide an identifier (accession, DOI, RRID) for any resource other than the study's own dataset. [majority verdict 'no' (4/5 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":50.0,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not state any licence for the data; the CC BY-NC licence noted applies to the article, not the dataset.","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":1.0,"verdict":"yes","evidence":"Imaging was performed using a Leica DMi8 microscope equipped with a Yokogawa CSU-W1 spinning disk, an Andor Zyla 4.2 Plus sCMOS camera, a Leica 63 ×1.40-NA oil objective, a motorized stage (ASI MS2000), and Semrock filters.","grounded":true,"rationale":"Specific instruments and software are named, providing provenance information. [majority verdict 'yes' (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":0.5,"verdict":"partial","evidence":"Table S1 details marker gene information, while Videos S3–S5 illustrate the spatial localization of cell types across seqFISH embryos, alongside imputed gene expression patterns and high-resolution clustering.","grounded":true,"rationale":"Variable-level definitions (marker gene info) are provided in a supplementary table within the article, but no documentation object (README, codebook) is said to accompany the data deposit. [majority verdict 'partial' (3/5 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 for the dataset; the Zenodo link likely includes versioning but it is not stated in the paper.","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":1.0,"verdict":"yes","evidence":"Scripts for analysis and figure panels in this manuscript are available at https://github.com/ltgharland/Spatiotemporal-Atlas-of-Mouse-Gastrulation .","grounded":true,"rationale":"A machine-resolvable code repository URL (GitHub) is given for the study's own code. [majority verdict 'yes' (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":"S.G. was supported by a Royal Society Newton International Fellowship (NIF\\R1\\181950), Australian Research Council DECRA Fellowship (DE220100964), and Chan Zuckerberg Initiative Single Cell Biology Data Insights grant (2022-249319).","grounded":true,"rationale":"Award numbers are given for the funding. [majority verdict 'yes' (3/5 passes agreed)]","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":"The paper does not state any licence for the data; the CC BY-NC licence noted applies to the article, not the dataset.","gain":16.67,"priority":"essential","scored":true},{"key":"f_dataset_pid","dimension":"F","label":"Persistent identifier for the data","action":"Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"DAPI images, molecules, and segmentation boundaries can be downloaded from Zenodo at https://zenodo.org/records/13977985 .","why":"The only identifier for the dataset is a URL (https://zenodo.org/records/13977985), which is not a PID scheme string (DOI, Handle, ARK, URN, or repository accession) as defined in the rubric. [majority verdict 'partial' (3/5 passes agreed)]","gain":8.33,"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 (open or proprietary) is named for the released data; the paper only describes the data as 'seqFISH images' and 'processed data' without specifying formats.","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":"DAPI images, molecules, and segmentation boundaries can be downloaded from Zenodo at https://zenodo.org/records/13977985 .","why":"The dataset identifier (Zenodo URL) appears only in the body text of the Data Availability Statement and Key Resources Table, not as a reference-list entry. [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 for the dataset; the Zenodo link likely includes versioning but it is not stated in the paper.","gain":4.17,"priority":"useful","scored":true},{"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":"no","current":0.0,"evidence":"seqFISH on a total of 20 optical sagittal sections from four embryos (five optical sections/embryo) that were collected at E6.5 and E7.5 (Figures 1A–1E and S1A; Videos S1 and S2). After sample preparation, imaging, cell segmentation, and mRNA dot calling, we computed normalized gene expression levels for 351 genes across 14,794 cells (Figure 1E).","why":"The dataset's content and extent are described in running prose (number of sections, embryos, genes, cells) but there is no itemised inventory such as a Data Records section or table listing files or variables. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 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":"partial","current":0.5,"evidence":"DAPI images, molecules, and segmentation boundaries can be downloaded from Zenodo at https://zenodo.org/records/13977985 .","why":"The paper describes an action (download from Zenodo) without applying an explicit access-level label, so the access level must be inferred. [majority verdict 'partial' (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 community data or metadata standard (e.g., MIAME, MIxS, BIDS, an ontology) is named as being applied to the data; only manuscript reporting guidelines may be present but not for the data.","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":"partial","current":0.5,"evidence":"Table S1 details marker gene information, while Videos S3–S5 illustrate the spatial localization of cell types across seqFISH embryos, alongside imputed gene expression patterns and high-resolution clustering.","why":"Variable-level definitions (marker gene info) are provided in a supplementary table within the article, but no documentation object (README, codebook) is said to accompany the data deposit. [majority verdict 'partial' (3/5 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 from mouse embryos, not human subjects, so no gatekeeper is named; the paper does not address sensitive data access.","gain":0.0,"priority":"useful","scored":false},{"key":"i_qualified_references","dimension":"I","label":"Identifiers for the resources the data depend on","action":"Cite by identifier every resource the data depend on — the source datasets' accessions, the reference build (GRCh38 / GCA_000001405.28), the cohort application number, the code DOI — and register those relations on the dataset record (IsDerivedFrom, IsSupplementTo). A name is not a link: it cannot be resolved, versioned, or followed by a machine.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper cites external resources (e.g., other atlases, software) but does not provide an identifier (accession, DOI, RRID) for any resource other than the study's own dataset. [majority verdict 'no' (4/5 passes agreed)]","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":"The paper does not mention any temporal commitment: neither a retention period nor an availability timing.","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.","Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","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.","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":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T12:37:55.465449Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}