brycewang-stanford Data & Code Availability (pnas-data)
When to trigger
- There is no Data Availability Statement, or it says "available on request".
- Sequences/structures/datasets are not deposited or have no accession numbers.
- Custom analysis code is not in a public, archived repository.
- Unique reagents/strains/cell lines have no sharing plan.
PNAS's standard (the bar)
PNAS requires a Data Availability Statement in every research article, and that the data and materials needed to support the conclusions be deposited and available at the time of submission/publication. For data types with an established public repository, deposition is required, and the accession numbers/DOIs go in the Data Availability Statement. "Available upon request" is not sufficient for the primary data underlying the figures and conclusions.
Deposit in approved repositories (with accessions)
| Data type | Deposit in (examples) |
|---|---|
| Nucleotide / genome sequences | GenBank / ENA / DDBJ |
| High-throughput sequencing | GEO / SRA / ArrayExpress |
| Protein/macromolecular structures | PDB; maps → EMDB |
| Proteomics | PRIDE / ProteomeXchange |
| Crystallographic data | CCDC / CSD |
| Generic datasets | Dryad / Zenodo / Figshare / OSF |
| Code | GitHub/GitLab + archived to Zenodo (DOI) |
- Obtain accession numbers / DOIs before/at submission; cite them in the Data Availability Statement and Materials and Methods.
- Code that produces the results must be public and archived (a versioned release with a citable DOI; a bare GitHub link is not durable).
Data Availability Statement (template)
All study data are included in the article and/or SI Appendix. [Sequencing data have been deposited in GEO (accession GSEXXXXXX).] [Structures have been deposited in the PDB (XXXX).] [Analysis code has been deposited in Zenodo (DOI: 10.5281/zenodo.XXXXXXX).] [Previously published data used in this work are available at …] [Restricted data (e.g., human-subjects data) are available under … from … subject to …]
Avoid bare "data available on request" for primary data; restricted human/clinical data must state the access procedure and the controlling body.
Where the statement and the data live
- The Data Availability Statement is a required element of the article (near the end, before/with the references — confirm placement in current guidelines).
- Datasets too large for a figure but central to the conclusions can go in SI Appendix or, if very large, in an external repository cited by accession/DOI — not "available on request."
- Reference the deposited data in both the Data Availability Statement and the Materials and Methods, so a reader following the methods can reach the data.
Materials & reagents
- Unique materials (plasmids, cell lines, strains, antibodies) should be available, e.g., via Addgene/repositories or under an MTA; state how.
- Identify key reagents with RRIDs where available.
Ethics & compliance (as applicable)
- Human-subjects: IRB/ethics approval + informed consent statement.
- Animal work: IACUC/animal-ethics approval and guideline compliance.
- Field/biodiversity: permits and the Nagoya Protocol where relevant.
- Dual-use / biosafety: flag if applicable.
Output format
【Data deposited】 type → repository → accession/DOI (list each) | gaps
【Code public + archived DOI】 yes/no (link + DOI)
【Data Availability Statement】 drafted? compliant (no "on request" for primary data)?
【Materials sharing】 plan for unique reagents (Addgene/MTA)
【Ethics approvals】 IRB / IACUC / permits present where needed?
【Next】 pnas-significance
Anti-patterns
- Do not write "data available on request" for the primary data behind the figures.
- Do not link only to a personal/lab website (not durable) — use an archival repository with a DOI.
- Do not forget to make code public and versioned; reviewers may try to run it.
- Do not submit without accession numbers in hand for deposited data.