A spatiotemporal atlas of mouse gastrulation and early organogenesis to explore axial patterning and project in vitro models onto in vivo space

“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 .”

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)]

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

“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).”— not found in the paper; verdict downgraded

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)]

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'

“DAPI images, molecules, and segmentation boundaries can be downloaded from Zenodo at https://zenodo.org/records/13977985 .”

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)]

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

The data are from mouse embryos, not human subjects, so no gatekeeper is named; the paper does not address sensitive data access.

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

The paper does not mention any temporal commitment: neither a retention period nor an availability timing.

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 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.

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'

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)]

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'

“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.”

Specific instruments and software are named, providing provenance information. [majority verdict 'yes' (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

“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.”

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)]

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