Nature Immunology Formatting Requirements: Complete Author Guide

The Nature Immunology Content Types page describes the Article abstract as up to 150 words and unreferenced.

• Word limit: 150 words maximum (100-150 words for a Resource)

• Citations: Not allowed in the abstract (it is unreferenced)

• Abbreviations: Spell out at first use in the abstract

For immunology papers, the abstract should specify the model system (mouse strain, human cohort, in vitro system), the key immune cell types or pathways studied, and the main finding with mechanistic detail. Don't just say "we identified a new role for T cells in disease X." Say "we found that CD8+ tissue-resident memory T cells in the lung drive chronic inflammation through IL-17A production independent of TCR engagement."

Quantitative results belong in the abstract. If your key finding is a fold change in cytokine levels or a difference in disease score, include the numbers. Immunology is increasingly quantitative, and vague language in the abstract signals imprecise experiments.

One immunology-specific tip: avoid starting the abstract with "The immune system plays a central role in..." or similar generic statements. Reviewers at this level know what the immune system does. Start with the specific problem.

Nature Immunology allows up to 8 display items (figures and tables combined) in the main text.

Figure specifications:

Extended Data: Up to 10 Extended Data figures or tables. Peer-reviewed and published alongside the article. Don't count toward the 8-item main display limit. For immunology papers, Extended Data typically contains additional FACS panels, histology images, supporting cytokine measurements, and additional gating panels.

Flow cytometry figures: For flow cytometry experiments, the Nature Portfolio Reporting Summary asks you to describe the gating strategy and to confirm that a figure exemplifying it is provided in the Supplementary Information. A full gating figure showing all sequential gates used to define the populations analyzed is the practical way to meet that, and it typically includes:

• Forward scatter / side scatter gate (to exclude debris)

• Singlet gate (to exclude doublets)

• Live/dead discrimination

• Lineage marker gates leading to the population of interest

• The final analytical gate shown in the figure

The Reporting Summary places the exemplifying figure in the Supplementary Information, so put it there even if you also show the final gate in a main figure.

Microscopy figures: For fluorescence microscopy and confocal images, include scale bars with explicit measurements. State the objective magnification and numerical aperture in the figure legend. If images have been adjusted for brightness or contrast, state this in the Methods.

Nature Immunology uses the standard Nature citation style.

In-text citations: Superscript numbers, numbered in order of first appearance. Multiple citations separated by commas (e.g., "^1,2"), ranges with hyphens (e.g., "^3-7").

Reference list format:

1. Smith, A. B., Johnson, C. D. & Williams, E. F. Title of article. Nat. Immunol. 26, 123-130 (2025).

Key formatting details:

• Author names: Last name, comma, initials with periods, as in the journal's examples

• "&" before the last author

• Journal names abbreviated, as in the journal's examples

• Volume in bold

• No issue numbers for most journals

• Year in parentheses

• DOIs encouraged but not required in the reference list

The reference guideline for Articles is up to about 50, which reflects the need to cite prior immunological studies, mouse model characterizations, and the extensive literature on most immune pathways.

Number references in the order the journal's AIP and formatting page gives: main text, tables, figure legends, boxes, Methods, the Data Availability section, then Extended Data. Methods-only references continue the numbering and accompany the additional Methods at the end of the paper.

A practical note for immunology authors: the journal's AIP and formatting page does not state how many authors to list per reference, so follow its examples, and budget your reference count with consortium and Human Cell Atlas papers in mind.

Nature Immunology uses the standard Nature Portfolio tiered system.

Extended Data (Tier 1): Up to 10 figures or tables. Peer-reviewed. This is where additional FACS plots live if they don't fit in the main figures; the gating-strategy figure requested through the Reporting Summary goes in the Supplementary Information. Also common: additional phenotyping data, time-course experiments, and results from secondary disease models.

Supplementary Information (Tier 2): Downloadable files. Supplementary Tables (typically Excel format for large datasets), Supplementary Figures, Supplementary Notes, and Supplementary Videos.

Source Data (Tier 3): Raw data underlying each figure. The journal encourages source data for figures whenever possible and requires full-length, unprocessed gels and blots as source data for any relevant figures.

Immunology-specific data requirements:

• Single-cell RNA-seq data fall under Nature Portfolio's mandatory deposition list for DNA and RNA sequencing data (for example, the NCBI Sequence Read Archive) and gene expression data (GEO or ArrayExpress), with accession numbers provided in the paper

• Flow cytometry data (FCS files) should ideally be deposited in FlowRepository or a similar public repository

• Bulk RNA-seq and ChIP-seq data go in GEO with appropriate metadata

• Proteomics data should be deposited in PRIDE or equivalent

The Reporting Summary is required for life-sciences research articles sent for review and covers antibody validation, cell line authentication, animal study reporting, and statistical methods. It's made available to editors and reviewers during assessment and published with accepted manuscripts.

Nature Immunology follows the standard Nature Portfolio manuscript structure. The manuscript should begin with:

• Title (concise; the journal says titles and abstracts should be easily understood by any scientist)

• Author names with superscript affiliation numbers

• Affiliations with full institutional addresses

• Corresponding author(s) with email addresses

• ORCID iDs (the journal asks corresponding authors of accepted papers to provide one before the final version is submitted; encouraged for co-authors)

Uploaded separately:

• Cover letter

• Reporting Summary (requested for life-sciences manuscripts sent for peer review)

• Conflict of interest declarations (in the submission system)

• Competing interests statement

The cover letter is important for Nature Immunology because the journal's scope spans innate immunity, adaptive immunity, mucosal immunology, tumor immunology, and more. Clearly position your work within the journal's scope and explain why the findings matter to a broad immunology audience, not just specialists in your subfield.

Nature Immunology has several formatting and editorial conventions that aren't immediately obvious from the general Nature Portfolio guidelines.

1. Flow cytometry gating strategies are requested through the Reporting Summary. The Reporting Summary asks you to describe the gating strategy for flow cytometry experiments and to confirm that a figure exemplifying it is provided in the Supplementary Information. Show the gating sequentially, from scatter gates through to the final analytical population, and include FMO (fluorescence minus one) controls for any marker where gating boundaries aren't obvious.

2. Antibody validation is scrutinized. For every antibody used, the Reporting Summary asks for the antibodies used and how they were validated. Nature Immunology reviewers, particularly for papers using novel or uncommon antibody clones, will ask for evidence of specificity. Include catalog numbers, clone names, and RRIDs for all antibodies in the Methods.

3. Mouse model reporting has specific requirements. State the strain, sex, age, and vendor for all mice. Specify housing conditions (SPF, conventional) and any breeding schemes. For disease models, describe the model induction protocol with enough detail that another lab can reproduce it. If you used only one sex, explain why.

4. The 8-display-item limit is generous but not infinite. With flow cytometry-heavy papers, it's easy to fill 8 figures with FACS plots alone. Build your figures strategically. Each main figure should address a distinct question in the story, not just show another marker or time point. Supplementary FACS data belongs in Extended Data.

5. Single-cell data presentation has evolving standards. For scRNA-seq experiments, Nature Immunology expects UMAP/tSNE plots with clearly labeled clusters, marker gene expression overlays, and statistical comparisons between conditions. Provide the clustering parameters, dimensionality reduction settings, and quality control thresholds in the Online Methods. Include the number of cells analyzed before and after QC filtering.

6. Statistics for immunology experiments. For in vivo experiments, state the number of mice per group, not just "n = 5." If you pooled cells from multiple mice, state how many mice were pooled and how many independent experiments were performed. Nature Immunology distinguishes between technical replicates (repeated measurements of the same sample) and biological replicates (independent mice or donors), and reviewers will ask for clarification if this is ambiguous.

7. Report sex. The Nature Portfolio Reporting Summary has a "Reporting on sex" section for animals and other research organisms and a "Reporting on sex and gender" section for studies with human participants or human data. Complete these fields and explain a single-sex design rather than leaving sex unaddressed. This applies to both in vivo mouse studies and human cohort analyses.

8. Wide relevance is one of the editorial criteria. Nature Immunology's editorial process page lists the degree to which a paper advances understanding of the field, the soundness of its conclusions, the evidence supporting them and their wide relevance to the readership as the basis for deciding whether to send it for review. A technically excellent paper focused on a narrow immune subset in a highly specific disease context may be desk-rejected if the editors cannot identify broad relevance. The cover letter must address who in the broader immunology community (not just your subfield) would find the result meaningful.

9. Plan data deposition early. Nature Portfolio's policy makes deposition in a community repository mandatory for certain data types (including DNA and RNA sequencing data, gene expression data and proteomics data), requires accession numbers to be provided in the paper, and says supporting data must be made available to editors and peer reviewers where requested at the time of submission. Have GEO accession numbers for sequencing data ready before you submit. Flow cytometry data are not on the mandatory list, but the policy names public repositories as the preferred way to share data.

Nature Immunology's formatting requirements combine Nature Portfolio standards with immunology-specific demands around flow cytometry gating, antibody validation, and data presentation. A missing gating-strategy figure is easy to prevent with proper preparation.

For an overview of Nature Immunology's scope, impact factor, and editorial identity, see the Nature Immunology journal profile. A Nature Immunology submission readiness check checks your formatting against Nature Immunology's specific requirements, catching issues like missing structural elements, reference style errors, and word count overruns. It's a fast way to verify that you've covered the basics before entering the submission system.

For related journals in the Nature Portfolio, see our Nature formatting requirements guide and Nature Genetics formatting guide. You can also explore our full collection of journal submission guides for additional resources.

For manuscripts targeting Nature Immunology, four patterns generate the most consistent desk-rejection outcomes.

Missing or incomplete flow cytometry gating strategy. The Reporting Summary asks for a figure exemplifying the gating strategy in the Supplementary Information for flow cytometry experiments. Sequential gating from scatter gates through live/dead discrimination through lineage markers to the final analytical population is the clearest way to provide it. Papers with FACS data that only show the final analytical plots, without showing how that population was defined, invite requests for the missing gating.

This is an easily preventable revision trigger. Include FMO controls for any marker where the gating boundary is not unambiguous.

Scope mismatch: specialist findings without broad immunology community relevance. Nature Immunology's editorial process page lists the advance made, the soundness of the conclusions, the supporting evidence and wide relevance to the readership as the basis for sending a paper to review. The journal covers all areas of immunology, and papers must speak across subfields.

A mechanistically detailed characterization of a regulatory pathway in a narrow cell subset in a single disease model will face desk rejection unless the editors can identify why a researcher working on a different immune cell type, tissue, or disease would find the result meaningful. The cover letter must make this case directly. "This will interest researchers in [subfield]" is not enough.

Phenotypic finding without mechanistic resolution. Nature Immunology expects mechanistic depth for Articles and Resources. Papers that demonstrate that a gene knockout produces an immunological phenotype without explaining how the gene mediates that phenotype routinely face desk rejection. The bar is: you showed that X knockout mice have fewer memory T cells; the reviewers want to know the molecular mechanism by which X normally supports memory T cell survival or formation. Correlative in vivo data establish the phenomenon; mechanistic experiments (genetic rescue, epistasis, molecular interaction data) establish the story.

Supplementary figure overload as a substitute for editorial clarity. A manuscript with 4 main figures and 12 supplementary figures can signal that the main story is not clearly organized. The journal's guidance says only Supplementary Information relevant to the conclusions should be included, that Supplementary Figures should be used only when Extended Data is not appropriate, and that authors are encouraged to be selective. Supplementary material should be genuinely supplementary to the main story, not data that would have been figures 5 through 8 had the display-item limit allowed it.

A Nature Immunology pre-submission readiness check evaluates whether your manuscript meets the gating, mechanistic, and scope requirements that determine desk-rejection risk.