Agent Skills
› brycewang-stanford/Awesome-Journal-Skills
› cc-reporting-standards
cc-reporting-standards
GitHub用于组装Cell Press论文的STAR Methods和关键资源表，确保实验严谨性与可重复性。涵盖细胞系鉴定、抗体验证、ARRIVE动物报告及数据代码归档规范，指导方法部分撰写与审计，不设计实验。
触发场景
起草或审核Cell Press投稿的方法部分
构建关键资源表并分配RRID
应对审稿人对未认证细胞系或缺失数据的质疑
需要结构化报告动物或测序工作的严谨性
安装
npx skills add brycewang-stanford/Awesome-Journal-Skills --skill cc-reporting-standards -g -y
SKILL.md
Frontmatter
{
"name": "cc-reporting-standards",
"description": "Use when assembling STAR Methods and the Key Resources Table for a Cancer Cell (Cell Press) manuscript, and when ensuring rigor \/ reproducibility (cell-line authentication, mycoplasma, antibody validation, ARRIVE animal reporting, data\/code deposition). It governs reporting; it does not design experiments."
}
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:
- Key Resources Table (KRT) — at the top; tabulates every critical reagent/resource with source, identifier, and RRID.
- Resource availability — Lead contact; Materials availability (plasmids, cell lines, mouse strains); Data and code availability.
- Experimental model and study participant details — cell lines, animals, human subjects, organoids/PDX provenance.
- Method details — full protocols, reproducible by an expert.
- Quantification and statistical analysis — what test, what
n, what software (links tocc-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:
- Is the KRT at the top, with a row for every antibody, line, organism, plasmid, oligo, dataset, and software?
- Does Resource availability name the lead contact and state materials + data + code availability explicitly?
- Are cell lines authenticated (STR), mycoplasma-negative, and cross-checked against the ICLAC misidentified-lines register?
- Do animal subsections give species/strain/sex/age, sample-size rationale, randomization, and blinded outcome scoring?
- Are all newly generated large datasets deposited with accessions echoed in both the KRT and the availability statement?
- Is the statistics subsection specific — exact test,
nas 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
版本历史
- 1839142 当前 2026-07-05 12:26
