cc-reporting-standards

Rigor, Reproducibility & STAR Methods (cc-reporting-standards)

When to trigger

• Drafting or auditing the Methods section for a Cell Press submission
• Reviewers may flag unauthenticated cell lines, undefined reagents, or missing deposition
• Need to build the Key Resources Table (KRT) and assign RRIDs
• Animal or sequencing work needs structured rigor reporting

STAR Methods structure

Cell Press uses STAR Methods (Structured, Transparent, Accessible Reporting). Organize methods under standardized headings:

1. Key Resources Table (KRT) — at the top; tabulates every critical reagent/resource with source, identifier, and RRID.
2. Resource availability — Lead contact; Materials availability (plasmids, cell lines, mouse strains); Data and code availability.
3. Experimental model and study participant details — cell lines, animals, human subjects, organoids/PDX provenance.
4. Method details — full protocols, reproducible by an expert.
5. Quantification and statistical analysis — what test, what n, what software (links to cc-statistics).

Key Resources Table — what must carry an RRID / identifier

Category	Required detail
Antibodies	Host, clone, vendor, catalog #, RRID, dilution/application
Cell lines	Name, sex/origin, source, authentication status, RRID (Cellosaurus)
Chemicals / inhibitors	Vendor, catalog #, identifier
Critical kits	Vendor, catalog #
Deposited data	Repository + accession (GEO/SRA/PRIDE/PDB)
Oligos / sgRNAs / primers	Full sequences
Recombinant DNA / plasmids	Source, Addgene # / RRID
Organisms / strains	Strain, source, RRID (e.g., MGI/JAX)
Software / algorithms	Name, version, URL, RRID

Cell-line rigor (frequent reviewer target)

• Authenticate human cell lines (STR profiling); reference Cellosaurus; state the source.
• Mycoplasma testing — state that lines were tested negative; give frequency.
• Flag any misidentified/commonly contaminated lines (ICLAC register) and justify use.
• Report passage range and culture conditions enough to reproduce.

Antibody validation

• Give clone, catalog, RRID, and application-specific validation (KO/KD control, single band of expected MW, IHC titration with positive/negative tissue).
• For new/critical antibodies, show validation in the supplement.

Animal reporting (ARRIVE 2.0 essentials)

• Species, strain, sex, age, source; housing and husbandry.
• Sample size rationale; randomization; blinding of outcome assessment.
• Inclusion/exclusion criteria; humane endpoints; number used and analyzed.
• IACUC protocol number and approving institution (statement routed via cc-ethics-registration).

Data and code availability

• Deposit and cite accessions in the KRT and availability statement:
  • Sequencing / arrays → GEO/SRA; controlled human genomics → dbGaP/EGA
  • Proteomics → PRIDE; metabolomics → MetaboLights/Workbench
  • Structures → PDB (+ EMDB for cryo-EM maps)
• Custom code → versioned public repo with a citable DOI (e.g., Zenodo).
• "Available on request" is unacceptable for these data types.

Checklist

• STAR Methods headings used; KRT at top
• Every antibody, cell line, organism, plasmid, software has source + RRID
• Human cell lines STR-authenticated; mycoplasma-negative stated
• Antibody validation described (and shown for critical ones)
• Animal section reports sample size, randomization, blinding, exclusions
• All large datasets deposited; accessions in KRT + availability statement
• Custom code deposited with DOI
• Lead contact and materials-availability statements present

Anti-patterns

• Cell lines with no authentication or mycoplasma statement
• Antibodies listed as "anti-X (Abcam)" with no catalog/RRID/validation
• Animal methods with no randomization/blinding/sample-size basis
• Sequencing data "available upon request" with no accession
• Methods too thin to reproduce the experiment

Output format

【STAR Methods】headings complete? KRT present?
【KRT gaps】reagents missing source/RRID: [...]
【Cell-line rigor】authenticated? mycoplasma? contaminated-line flags?
【Antibody validation】adequate / show in supplement: [...]
【Animal rigor】ARRIVE elements present? [...]
【Deposition】GEO/SRA/PRIDE/PDB accessions + code DOI status
【Next step】cc-statistics or cc-ethics-registration