--- name: molcell-submission description: Use as the final preflight before submitting to Molecular Cell — a complete checklist across mechanism, single-mechanism arc, length budget, figures, STAR Methods, data deposition, numbered references, front-matter artifacts, and required files. Bundles the checklist and cover-letter templates. --- # Submission Preflight & Cover Letter (molcell-submission) ## When to trigger - The manuscript is "done" and you're about to upload to Editorial Manager. - You want a single gate confirming every other molcell-* skill's output landed. - A revision is going back and you need to confirm nothing regressed. ## Master preflight checklist ### Mechanism & narrative - [ ] Clears the deep-mechanism bar (`molcell-fit` rung ≥ 3; orthogonal validation; physiological relevance). - [ ] Single-mechanism arc (question → mechanism → physiological consequence); no technique catalog. - [ ] Separation-of-function / point-mutant evidence ties the mechanism to the phenotype. - [ ] Title is declarative, names the molecular actor + molecular action. ### Length & structure - [ ] Main text ~7,000 words incl. main figure legends (or ~4,000 for a Short Article); confirm live cap. - [ ] Display items within ~7; extras in Supplemental Information. - [ ] Results have molecular-claim subheadings; Discussion interpretive (model + excluded alternative), not a recap. ### Front-matter artifacts - [ ] **Highlights**: 3–4 bullets, each ≤ 85 characters incl. spaces. - [ ] **eTOC / In Brief blurb**: ~50 words, third person, accessible language. - [ ] **Graphical Abstract**: single panel, clear flow, minimal text, RGB, correct size. - [ ] **Summary**: single paragraph (~150 words), mechanism named, ≥1 quantified result, no citations. ### Figures & display items - [ ] Sized to 85 / 114 / 174 mm; min font ~6–7 pt; RGB. - [ ] Data shown (points + n + replicate type); error bars defined; primary data (gels/traces/maps) shown. - [ ] Blot integrity: uncropped key blots in supplement; source scans retained; splices disclosed. - [ ] Structures: resolution/FSC/refinement reported; contacts supported by density. - [ ] Genomics: normalization + replicate metric stated; colorblind-safe throughout. ### STAR Methods - [ ] **Key Resources Table** complete (antibodies w/ Cat#+RRID; plasmids/oligos/purified proteins; deposited data w/ accession; software w/ version). - [ ] **Resource Availability**: Lead Contact / Materials Availability / Data and Code Availability. - [ ] Experimental Model and Subject Details incl. ethics (IRB/IACUC, consent, authentication, mycoplasma). - [ ] Method Details reproducible (purification/reconstitution/pipelines); **Quantification and Statistical Analysis** consolidated. ### Data & code - [ ] Data deposited (GEO/PDB+EMDB/PRIDE); accession numbers/DOIs in hand; mirrored into KRT "Deposited Data." - [ ] Structures deposited with maps/structure factors; code public + archived (Zenodo/Mendeley DOI). - [ ] Data and Code Availability statement complete (data / code / additional). ### References - [ ] Cell Press **numbered** superscript in text, in order of first appearance. - [ ] Reference list numbered by appearance; full author lists; abbreviated journal names. - [ ] Every superscript resolves to one entry; no uncited entries; single merged list incl. STAR Methods. ### Required files & metadata - [ ] Main text (Summary, Intro, Results, Discussion, STAR Methods, legends, references). - [ ] Figures at required resolution + legends; Graphical Abstract file. - [ ] Highlights and eTOC blurb files/fields. - [ ] Supplemental Information (figures/tables/videos + captions). - [ ] Cover letter (mechanistic-advance forward). - [ ] Authors, affiliations, ORCIDs, corresponding author, **Lead Contact**. - [ ] CRediT author contributions; competing interests; funding. - [ ] Suggested / opposed reviewers (if used). ## Final integrity sweep - [ ] No over-interpretation beyond the evidence (re-read Summary + Discussion + structure claims). - [ ] Every figure's n, replicate type, error bar, and test defined and consistent with QSA. - [ ] All accession numbers/DOIs live and correct; structure map-model fit matches the deposited entry. - [ ] Single-blind by default — do not anonymize unless double-blind requested. Confirm on the portal. ## What the desk editor is deciding Submission goes through Cell Press Editorial Manager to an in-house scientific editor who makes the review-or-reject call before any referee sees the file. Two things they cannot recover later must be right at upload: the *mechanistic depth* (is the molecular event proven, or only proposed) and the *orthogonal validation* (are the independent lines already in the manuscript, not promised in a rebuttal). The cover letter exists to state both in the editor's vocabulary. Everything else in the preflight is hygiene; these two are the gate. Do not open the cover letter with "Please find enclosed our manuscript." Open with the mechanism. A serviceable first sentence: *"We show that [molecular actor] [molecular action] by [mechanistic detail], resolving how [process] is controlled and why [physiological outcome] depends on it."* Then one short paragraph naming the orthogonal lines of evidence (e.g., structure + reconstitution + separation-of-function genetics), one sentence on why Molecular Cell's mechanism-focused readership specifically, and — if relevant — a candid line on concurrent related work. Keep it to a page. ## Revision-specific gate When a revised manuscript goes back, run the checklist again but add: every promised experiment from the response letter is now *in* the paper or explicitly justified as out of scope; every referee-driven change is reflected in both text and figures (a common regression is updating a panel but not its legend or the QSA block); the response letter and the manuscript agree on every number; no new mechanistic claim crept in without new evidence; and any re-processed structure/genomics matches the deposited entry. Version figures so an old panel cannot ship by accident. ## Metadata traps specific to Cell Press - The **Lead Contact** is a distinct required role from the corresponding author and must match the Resource Availability statement exactly. - Molecular Cell uses **single-blind** review by default; do not strip author identity unless double-blind was explicitly requested — confirm the current option on the portal. - CRediT contributions, competing-interests, and funding statements must be structured fields, not only prose. - Accession numbers and the Zenodo/Mendeley code DOI must appear identically in the KRT "Deposited Data" rows, the Data and Code Availability statement, and any Editorial Manager metadata field. ## Templates - `templates/checklist.md` — copyable preflight checklist. - `templates/manuscript_template.md` — Molecular Cell manuscript skeleton (STAR Methods, KRT, eTOC blurb, Highlights, cover-letter scaffold). ## Output format ``` 【Blocking gaps】 [...] (must fix before upload) 【Warnings】 [...] (should fix) 【Files ready】 main / figures+legends / GA / Highlights+eTOC / SI / cover letter / metadata 【Verdict】 GO / NO-GO + the top 3 fixes 【Next】 submit | molcell-rebuttal (after decision) ``` ## Anti-patterns - **Do not** upload before accession numbers/DOIs (and deposited structures) exist. - **Do not** ship Highlights over 85 characters or an eTOC blurb in the first person. - **Do not** submit a free-text Methods section instead of STAR Methods. - **Do not** leave author–date citations unconverted — Molecular Cell is numbered. - **Do not** rely on memory; run the checklist top to bottom. > Confirm all caps and required files against the current Molecular Cell information-for-authors page before upload.