Summary
Supplements are directly relevant, linked resources that support (but aren’t required to read) the article. Done well, they boost transparency, reproducibility, and reuse; done poorly, they confuse and decay.
Start with the journal’s rules: scope, allowed file types/sizes, peer-review/copyedit status, hosting/indexing, and licensing/data-sharing mandates.
13 useful supplement types (with packaging tips): Extended Methods; Raw/Tidy Data (+ data dictionary); Supporting Tables (Table S1…); Extra Figures (Figure S1…); Video/Animation (MP4 + captions); Audio (WAV/FLAC + metadata); Code/Notebooks (DOI-tagged release, README, env file); Case Studies; Instruments/Surveys (PDF + machine-readable schema); Source Texts & Translations; Extended Notes/Proofs; Traditional Appendices; and a manifest listing all files, formats, sizes, and DOIs.
Label & link clearly: stable filenames, S-series numbering, in-text cues (e.g., “see Table S4”). Prefer open formats (CSV, PDF/A, PNG/TIFF, MP4), alt-text/captions, sensible sizes, and a README for every non-trivial file.
Ethics & FAIR: de-identify human data, honour consents/permissions, apply clear licences (CC BY/OSI), and deposit in DOI-issuing repositories (discipline-specific when possible). Cross-cite DOIs and versions/commit hashes.
QC checklist: relevance and in-text references; stable names/numbering + manifest; open, accessible formats; licences/permissions; runnable code with sample data; self-contained figures/tables; top-level README.
Exclude: new unreviewed analyses, redundant duplicates, proprietary-only formats, identifiable data without consent. Signpost in cover letter and at point-of-use within the paper.
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13 Examples of Supplementary Materials for Academic Journal Papers (Plus How to Do Them Well)
Supplementary materials have become a core component of modern scholarly publishing. Digital platforms give journals the capacity to host rich, diverse artefacts—datasets, code, videos, extended methods—that simply won’t fit in a page-limited article. When used thoughtfully, supplements enhance transparency, reproducibility, and reader engagement. When used poorly, they become a dumping ground that confuses reviewers and risks long-term accessibility. This guide clarifies what counts as valid supplementary material, how to package it for your target journal, and offers 13 concrete examples you can adapt—along with naming, formatting, and compliance tips to avoid the most common pitfalls.
First Principles: What Journals Usually Mean by “Supplementary”
Across disciplines, journals broadly treat supplementary materials as directly relevant, clearly linked resources that support (but are not strictly required to understand) the main article. They add depth, verification, and reuse value without overwhelming the narrative. Terminology varies—supplemental material, supporting information, online appendix, auxiliary files—and policies differ on what is allowed, how it is reviewed, and which formats are acceptable.
Always start with the author guidelines. Pay attention to:
- Scope: What types are accepted? Any restrictions on new analyses or extra argumentation?
- File types & limits: Preferred formats (CSV, TXT, PDF, MP4), maximum sizes, one-file vs. many-files policy.
- Review & copyediting: Will the supplements be peer-reviewed or posted “as supplied by authors”?
- Indexing & hosting: Are supplements hosted on the publisher’s site, a repository, or both?
- Licensing & data sharing: Required licences (e.g., CC BY) and repository mandates.
13 Examples of Supplementary Materials (with Packaging Tips)
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Extended Methods (Detailed Protocols & Materials)
Keep the main paper’s Methods concise; move step-by-step protocols, reagent lists, instrument settings, pre-registration links, and deviation notes to a supplement.
Package it: A paginated PDF (Supplementary Methods) with section headings mirroring the article. Cross-reference from the main text (e.g., “see Supplementary Methods §2.3”). Include version numbers and dates.
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Raw Data, Datasets, and Databases
Provide machine-readable, tidy data (CSV/TSV, Parquet) with an accompanying data dictionary and README describing variables, units, missing-data codes, and processing steps.
Package it: If large, deposit in a trusted repository (e.g., institutional, field-specific) and supply a DOI in the supplement. For small datasets, upload as CSV plus a PDF Data Guide.
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Supporting Data Tables
Detailed numeric outputs, robustness and sensitivity checks, subgroup analyses, and additional descriptive statistics belong here.
Package it: Use a numbered scheme distinct from main tables (Table S1, S2 …). Provide concise titles and self-contained footnotes with units and abbreviations.
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Additional Figures, Graphs, and High-Resolution Images
Overflow visualisations, large maps, microscopy images, and alternative model plots that complement the main story.
Package it: Number as Figure S1, S2 … Include legends that restate key context (so the figure is interpretable when separated). Provide accessible alt-text if the journal supports it.
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Video & Animation (Procedures, Phenomena, Reconstructions)
Show techniques, behavioural responses, temporal changes, or model dynamics that are hard to convey in static images.
Package it: MP4 (H.264) is widely supported. Add captions, frame rate, resolution, and a one-paragraph description in a PDF index. Provide transcripts if audio matters for interpretation.
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Audio Files (Linguistics, Field Recordings, Signals)
Dialect exemplars, interviews (appropriately anonymised), bioacoustic signals, or sonifications of data.
Package it: Lossless (WAV/FLAC) if file sizes permit; otherwise, high-bitrate MP3. Supply metadata: speaker ID (pseudonym), location, date, device, sampling rate, consent status.
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Software, Code, and Computational Notebooks
Analysis scripts, simulation code, and notebooks that reproduce figures and results. Critical for transparency and reuse.
Package it: Deposit to a code repository with a tagged release and DOI (e.g., Zenodo + GitHub). Include
README.md,environment.yml/requirements.txt, and minimal test data. Reference the commit hash in the paper. -
Case Studies & Extended Exemplars
Rich qualitative vignettes, site descriptions, or extended examples that would crowd the discussion.
Package it: A clearly structured PDF with subheadings per case. Anonymise sensitive details and state your anonymisation protocol.
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Instruments: Questionnaires, Surveys, Forms
Provide the exact materials participants saw (layout, ordering, branching), plus scoring rules and validation references.
Package it: High-quality PDF facsimiles and a machine-readable version (CSV/JSON) of question text and response options. Include licensing terms if using proprietary scales.
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Source Texts & Translations
Original language passages, translations used for analysis, alignment tables, and translation notes.
Package it: Parallel columns in PDF for readability; separate UTF-8 text files for computational use. Clarify translation approach (literal, dynamic equivalence) and attest permissions where required.
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Extended Background & Contextual Material
Additional theoretical framing, derivations, proofs, instrument validation, or literature matrices that inform—but need not clutter—the main narrative.
Package it: A labelled Supplementary Note PDF (Note S1, S2 …) with cross-references from the article. Avoid introducing new, unvetted claims that weren’t peer-reviewed in the main paper.
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Traditional Appendices (Maps, Sketches, Charts)
Materials that historically lived in back-matter: expanded maps, site photos, coding schemes, decision trees.
Package it: Consolidate into Appendix S1 with a table of contents and figure/table numbering distinct from the main text.
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Comprehensive “List of Supplementary Files”
Many journals require a manifest. Even when not required, it helps reviewers and readers quickly understand the package.
Package it: A one-page PDF index (and a matching section in the cover letter) that lists each file with a 1–2 sentence description, format, size, and (if applicable) external DOI or URL.
File Naming, Numbering, and Cross-Referencing
Clarity lives in your filenames and labels. Use a stable convention that mirrors the order you reference in the paper:
- Filenames: PaperID_Supp_TableS1_MainOutcomes.csv, PaperID_Supp_FigureS3_ModelChecks.png, PaperID_Supp_Methods.pdf
- Numbering: Reserve “S” prefixes for supplements (Table S1, Figure S1, Note S1). Do not reuse main-text numbers.
- In-text cues: “Robustness results are reported in Table S4,” “See Figure S7 for alternative priors.”
Formats & Accessibility: Choose What Lasts
- Open, non-proprietary where possible: CSV/TSV, TXT/JSON/XML, PDF/A, PNG/TIFF, MP4 (H.264). Avoid locking essential data in PDFs only.
- Reasonable sizes: Compress sensibly; split massive files; use repositories for >100–500 MB assets.
- Accessibility: Provide alt-text for figures (if supported), captions and transcripts for A/V, readable font sizes, and high-contrast colour palettes.
- Documentation: Every non-trivial file should have a companion README that explains content, structure, and provenance.
Ethics, Consent, and Legal Considerations
- Human data: De-identify rigorously; follow consent terms for data sharing; state any access controls (e.g., controlled-access repositories).
- Third-party content: Secure permissions for images, instruments, or texts under copyright; document licences.
- Attribution & licences: Prefer clear, machine-readable licences (e.g., CC BY for documents, OSI-approved for code). Avoid “all rights reserved” unless mandated.
Repositories, DOIs, and the FAIR Principle
Many funders and journals expect data and code to be FAIR: Findable, Accessible, Interoperable, Reusable. Repositories issue persistent identifiers (DOIs) and improve discovery.
- Discipline-specific repositories: Use field-standard archives for better visibility and metadata richness.
- Institutional or generalist: When no community repository exists, use institutional archives or generalist platforms that support DOIs.
- Linking: Cite repository DOIs in the main paper and list them again in the supplements manifest. Match versions (e.g., “v1.1, commit 9f3e2ab”).
Quality Control: A Short Pre-Submission Checklist
- [ ] All supplementary items are directly relevant to the article’s claims and clearly referenced in-text.
- [ ] Files use stable, descriptive names; numbering follows S-series; a manifest is included.
- [ ] Formats are open where possible; files open on multiple systems; sizes are reasonable.
- [ ] Data are de-identified; consent and licences are honoured; permissions documented.
- [ ] Code runs from a clean environment with instructions; sample data or stubs are provided.
- [ ] Figures/tables are self-contained (titles, units, legends, abbreviations defined).
- [ ] A README at the top level explains folder structure and how supplements map to the paper.
Example Manifest (Template You Can Reuse)
Supplementary Materials – Manuscript: “Title of Paper”
S1 Supplementary Methods (PDF, 14 pp)
Detailed protocols; reagent lists; instrument settings.
S2 Table S1 – Descriptive Statistics (CSV, 38 KB)
Variable dictionary in S9.
S3 Figure S1 – Model Diagnostics (PNG, 2.1 MB)
Posterior predictive checks; priors in Note S1.
S4 Data – Cleaned Dataset v1.2 (DOI: 10.xxxx/xxxx)
Hosted in repository; see S9 for variable descriptions.
S5 Code – Analysis Release v1.2 (DOI: 10.xxxx/xxxx)
Reproducible pipeline; tested on Python 3.11; env file included.
S6 Video S1 – Procedure Demo (MP4, 90 s, 1080p)
Captioned; transcript in S8.
S7 Instrument – Survey Form (PDF, 6 pp) + JSON schema
Skip logic documented.
S8 Transcripts/Audio Metadata (PDF, 3 pp)
Anonymisation protocol; consent statements.
S9 Data Dictionary & README (PDF, 7 pp)
Codebook; units; missing data handling.
Smart Restraint: What Not to Include
- New, unreviewed analyses that materially change conclusions.
- Redundant copies of main-text figures/tables unless resolution requirements differ.
- Proprietary formats without an open alternative or viewer.
- Identifiable human data without explicit consent and safeguards.
Cover Letter & In-Paper Signposting
Help editors and reviewers navigate your materials:
- Cover letter: Include a concise paragraph listing supplements, why they’re included, and any repository DOIs.
- In-paper: Mention key supplements at the point of relevance (e.g., “Sensitivity outcomes are reported in Table S4”). Avoid burying all references in one paragraph.
Final Thought: Supplements as Scholarly Infrastructure
Think of supplementary materials as the scaffolding that supports your article’s claims—data that allow others to verify findings, methods that enable replication, artefacts that deepen understanding, and code that turns results into a living, reusable resource. Choose formats that last, document with the next researcher in mind, and align precisely with your journal’s expectations. Done well, your supplements won’t be “extra”; they’ll be the foundation of rigorous, transparent scholarship.
Need a second pair of eyes on your supplementary package—file formats, naming, readability, or repository readiness? Our academic editors can review for clarity, compliance, and coherence before you submit.
