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.

Worked micro-example: a KRT antibody row before → after

Before (desk-reject-grade entry):

> Anti-MARK7 — Abcam — for Western blot

After (STAR-compliant entry):

> Rabbit monoclonal anti-MARK7, clone EPR-xxxx, Abcam, Cat# ab000000, RRID:AB_0000000; WB 1:1000,

> validated against MARK7-KO lysate (single band at expected MW, Figure S1).

The "after" carries host, clonality, clone ID, vendor, catalog, RRID, application, dilution, and the

validation evidence — every column a Cancer Cell editor scans the KRT for. A reviewer who cannot find

the RRID or the KO/KD validation treats the reagent as unverified.

STAR Methods pre-submission self-check

Walk the Methods in the order an in-house editor will:

1. Is the KRT at the top, with a row for every antibody, line, organism, plasmid, oligo, dataset, and software?
2. Does Resource availability name the lead contact and state materials + data + code availability explicitly?
3. Are cell lines authenticated (STR), mycoplasma-negative, and cross-checked against the ICLAC misidentified-lines register?
4. Do animal subsections give species/strain/sex/age, sample-size rationale, randomization, and blinded outcome scoring?
5. Are all newly generated large datasets deposited with accessions echoed in both the KRT and the availability statement?
6. Is the statistics subsection specific — exact test, n as biological replicates, multiplicity correction?

Rigor failure modes that draw reviewer or editor flags

• A KRT that lists reagents but omits RRIDs or authentication status.
• Human lines with no STR profile, or a commonly contaminated line used without justification.
• Antibodies validated "by the manufacturer" only, with no in-house KO/KD or titration control.
• Animal work reporting "n mice" with no allocation, blinding, or exclusion criteria.
• Sequencing/proteomics described in Results but with no GEO/PRIDE accession by submission.
• Code described as "custom scripts" with no repository or DOI.

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