est-reporting-and-reproducibility

Reporting & Reproducibility (est-reporting-and-reproducibility)

ES&T strongly encourages public data and expects authors to make materials, data, and protocols available through public databases, with a data-availability statement and a Supporting Information file submitted alongside the manuscript and reviewed with it. Build these as you go, not the night before submission.

When to trigger

• Assembling the Supporting Information (SI) PDF/files
• Writing the data-availability statement and choosing repositories
• Depositing data, spectra, sequences, code, and protocols
• Making sure every figure/table can be regenerated from deposited data

What ES&T expects

1. Supporting Information. Submitted simultaneously as separate file(s); describe contents and file type in the SI paragraph (e.g., "Additional analytical methods, calibration data, and NMR spectra (PDF)"). Available to reviewers; free to readers on publication.
2. Data-availability statement. State where the data live and how to access them; cite accession codes / DOIs.
3. Public deposition by data type (see resources/external_tools.md):
   • Sequences → GenBank / ENA / DDBJ; omics/microarray → GEO / ArrayExpress; proteomics → PRIDE / ProteomeXchange; mass spectra → MassIVE / MetaboLights / MassBank.
   • General data/code → Dryad, figshare, Zenodo, OSF.
4. Methods reproducibility. Report instrument settings, reagents/standards, QA/QC, and analysis steps in enough detail to reproduce; deposit analysis code with seeds and pinned versions.
5. Restricted data. If data cannot be fully shared (privacy/legal), explain why and give README instructions on how to obtain it; provide what can be shared.

SI assembly checklist

• Extended methods, reagents/standards, instrument parameters
• Calibration curves, QA/QC tables (blanks, recoveries, CRMs, LOD/LOQ)
• Supplementary figures/tables/spectra referenced in order (Figure S1, Table S1…)
• Data-availability statement with accession/DOI
• Code/scripts deposited; figures regenerate from deposited data
• Page/word limits and file formats per ACS SI guidance (待核实 on specifics)

Deposition routing: data type → repository

ES&T expects deposition in the community-standard repository for each data type, not a generic catch-all. Reviewers in a sub-field know the canonical home and notice when data are not there (confirm any volatile mandate against the journal's current author guidelines — 待核实):

Data type	Expected repository	Reviewer's note if missing
DNA/RNA sequences	GenBank / ENA / DDBJ	not independently checkable
Omics / microarray	GEO / ArrayExpress	non-standard, hard to reuse
Proteomics	PRIDE / ProteomeXchange	unverifiable identifications
Mass spectra / metabolomics	MassIVE / MetaboLights / MassBank	spectra not reusable
General data / code	Dryad, figshare, Zenodo, OSF	"available on request" red flag

Worked micro-example (illustrative — SI for a PFAS fate study)

For the river-PFAS study, a reviewer-ready Associated Content package (illustrative) contains:

• SI PDF: extended LC-MS/MS methods, transition list and collision energies, the QA/QC table (field blanks, 92% recovery, per-analyte LOQ), calibration curves (R² > 0.99, illustrative), and the ROS censoring detail — each item S-numbered and referenced in order from the main text.
• Deposited: raw and processed concentration tables plus the analysis code (with the random seed for the bootstrap CI and pinned package versions) on Zenodo with a DOI; the mass spectra on MassIVE.
• Data-availability statement: "Concentration data and analysis code are available at Zenodo (DOI: 10.xxxx/illustrative); raw mass spectra are deposited at MassIVE (accession: illustrative)."

The test that catches drift: re-run the deposited master script on a clean machine — every figure and the 2.4 ng/L headline number must regenerate exactly. If they do not, the SI and manuscript have diverged.

Referee-pushback patterns and the venue-specific fix

• "Data available on request is not sufficient." → Deposit in the type-appropriate repository and cite the accession/DOI in the statement.
• "Methods not reproducible." → Move instrument settings, standards, and QA/QC into the SI in enough detail to repeat the work; deposit code with seeds and versions.
• "SI contents not described." → Write the SI paragraph naming each file and its type.

Anti-patterns

• "Data available on request" with no statement, repository, or accession
• An SI that is a dumping ground with no described contents or ordering
• Spectra/sequences/omics not deposited in the expected community database
• Code that does not run, or that cannot regenerate the manuscript's exhibits
• Leaving SI + deposition to submission day, so numbers drift from the manuscript

Output format

【SI contents】described + ordered (S-numbered)? [Y/N]
【Data-availability statement】present with accession/DOI? [Y/N]
【Deposition】data type → repository (GenBank/GEO/PRIDE/MassIVE/Dryad/Zenodo/OSF)
【Code】deposited, seeds + pinned versions, regenerates exhibits? [Y/N]
【Restricted data】justified + README to obtain? [N/A or Y/N]
【Next】est-writing-style

Supplementary resources

• ../../resources/external_tools.md — repositories by data type; reproducibility tooling
• ../../resources/official-source-map.md — data-availability and SI policy