cell-data

Business

Use to build Cell's data and code deposition plan and the Data and Code Availability statement that lives inside STAR Methods Resource Availability — approved repositories, accessions/DOIs at submission, and Cell's three-bullet availability format with Mendeley Data as Elsevier's default.

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How to use this skill

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Prompt to paste

I want to install this Agent Skill for this project in Codex.

Source SKILL.md: https://github.com/brycewang-stanford/Awesome-Journal-Skills/blob/HEAD/Cell-Skills/skills/cell-data/SKILL.md

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First, summarize what it does, its dependencies, license status if identifiable, and any risks. Show the exact files you propose to add under .agents/skills/cell-data/. Do not write files or run scripts until I approve.

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Data & Code Availability (cell-data)

When to trigger

There is no Data and Code Availability statement, or it says "available on request."
Sequences/structures/proteomics/datasets are not deposited or lack accessions.
Custom analysis code is not in a public, archived repository.
You need to draft the three-bullet statement for STAR Methods Resource Availability.

Where the statement lives

Cell's Data and Code Availability statement is a required subsection of Resource Availability inside STAR Methods (see cell-star-methods) — not a free-floating paragraph. Datasets deposited for this paper must also appear in the Key Resources Table under "Deposited Data."

Deposit in approved repositories (with accession/DOI)

Data type	Deposit in (examples)
High-throughput sequencing	GEO / SRA
Nucleotide / genome sequences	GenBank / ENA / DDBJ
Protein/macromolecular structures	PDB; cryo-EM maps → EMDB
Proteomics / mass spec	PRIDE / ProteomeXchange
Imaging / general structured datasets	BioStudies / BioImage Archive
Generic datasets (Elsevier default)	Mendeley Data, or Zenodo / Dryad
Plasmids / unique reagents	Addgene
Code (archive a release for a DOI)	GitHub/GitLab + Zenodo (citable DOI)

Mendeley Data is Elsevier's default repository and is the natural home for datasets without a dedicated community repository. Use a community repository (GEO, PDB, PRIDE) when one exists for the data type.

Obtain accession numbers / DOIs before submission; reviewers and editors expect them in hand.
Code that reproduces the results must be public and archived (a citable DOI via Zenodo) — a bare GitHub link is not durable.

Cell's three-bullet Data and Code Availability format

Cell uses a standardized three-statement block. Provide a sentence for each bullet:

Data and Code Availability

• [DATA] [Datatype] data have been deposited at [Repository] and are publicly
  available as of the date of publication. Accession numbers are listed in the
  Key Resources Table. / This paper analyzes existing, publicly available data
  [accessions in KRT]. / This paper does not report standardized datasets.

• [CODE] All original code has been deposited at [Zenodo/Mendeley Data] and is
  publicly available as of the date of publication. DOIs are listed in the Key
  Resources Table. / This paper does not report original code.

• [ADDITIONAL] Any additional information required to reanalyze the data
  reported in this paper is available from the Lead Contact upon request.

Each of the three bullets must be addressed even if the answer is "this paper does not report…". Restricted human/clinical data must state the controlled-access procedure and the controlling body.

Materials & ethics cross-links

Unique materials sharing belongs in Materials Availability (cell-star-methods); use Addgene/MTA and state how.
Ethics approvals (IRB/IACUC, consent, permits) belong in Experimental Model and Subject Details.
Identify key reagents with RRIDs in the Key Resources Table.

Output format

【Data deposited】 type → repository → accession/DOI (list each)  | gaps
【Code public + archived DOI】 yes/no (repo + Zenodo/Mendeley DOI)
【Three-bullet statement】 DATA ☐ / CODE ☐ / ADDITIONAL ☐ — all drafted?
【In KRT "Deposited Data"】 accessions listed? yes/no
【Restricted data】 controlled-access procedure stated where needed?
【Next】 cell-summary

Anti-patterns

Do not write "available on request" for the primary data behind the figures.
Do not link only to a personal/lab website — use an archival repository with a DOI.
Do not leave any of the three bullets unaddressed.
Do not forget to mirror accessions into the Key Resources Table.
Do not submit without accession numbers/DOIs in hand.

Confirm repository requirements and the exact three-bullet wording against current Cell Press / STAR Methods guidelines.