Nature Immunology Formatting Requirements: Complete Author Guide

Nature Immunology uses an unstructured abstract, consistent with all Nature Portfolio journals.

• Word limit: 150 words maximum
• Structure: Unstructured (single paragraph)
• Citations: Not allowed
• Keywords: Not submitted by authors
• 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 detailed gating strategies.

Flow cytometry figures: This is where Nature Immunology gets specific. Every flow cytometry figure must be accompanied by a full gating strategy showing all sequential gates used to define the populations analyzed. This 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 gating strategy can appear in the main figure (as a supplementary panel) or in Extended Data, but it must be present. The journal has been strict about this since approximately 2018, and it's the single most common reason for revision requests in flow cytometry-heavy papers.

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 without periods
• "&" before the last author
• Journal names abbreviated per ISO 4
• Volume in bold
• No issue numbers for most journals
• Year in parentheses
• DOIs encouraged but not required in the reference list

The reference cap for Articles is approximately 50. This is more generous than the main Nature journal (~30) and reflects the need to cite prior immunological studies, mouse model characterizations, and the extensive literature on most immune pathways.

References appear before the Online Methods section in the manuscript. The document order is: main text, references, Online Methods, figure legends, Extended Data.

A practical note for immunology authors: Nature style lists all authors in the reference list up to 6 authors; for papers with 7 or more authors, list the first 6 followed by "et al." Landmark consortium and Human Cell Atlas papers typically use et al. in references. Budget your reference count with this 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 most gating strategies live if they don't fit in the main figures. 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. Required for all main figures and Extended Data figures.

Immunology-specific data requirements:

• Single-cell RNA-seq data must be deposited in GEO or ArrayExpress with processed count matrices and raw FASTQ files
• 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 Life Sciences Reporting Summary is mandatory and covers antibody validation, cell line authentication, animal study reporting, and statistical methods. It's shared with reviewers and published alongside the paper.

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

• Title (concise, under 100 characters preferred)
• Author names with superscript affiliation numbers
• Affiliations with full institutional addresses
• Corresponding author(s) with email addresses
• ORCID iDs (required for corresponding author, encouraged for all)

Uploaded separately:

• Cover letter
• Life Sciences Reporting Summary (mandatory)
• 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 checked before peer review. Every flow cytometry experiment must have a complete gating strategy either in the main figures or Extended Data. The gating must be sequential, starting from scatter gates through to the final analytical population. Include FMO (fluorescence minus one) controls for any marker where gating boundaries aren't obvious. This is enforced by the editorial office before the manuscript is sent out for peer review: incomplete gating strategies are returned without reviewer input.

2. Antibody validation is scrutinized. For every antibody used, the Life Sciences Reporting Summary requires information about validation. 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. Sex as a biological variable must be addressed. The Nature Portfolio Reporting Summary explicitly asks how sex was determined and requires a justification if only one sex was used. If sex-based analyses were not performed, you must explain why in the Reporting Summary. This applies to both in vivo mouse studies and human cohort analyses. "Sex was not analyzed" without explanation is not acceptable.

8. Broad interest is a primary desk rejection criterion. Nature Immunology editors reject manuscripts on the basis of novelty and broad interest to the immunology community. 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. Data must be deposited before submission, not acceptance. Nature Immunology's editorial policy requires that data be deposited in public repositories and accession codes provided at the time of submission, not upon acceptance. Submitting without GEO accession numbers for sequencing data or FlowRepository identifiers for flow data will delay processing.

Nature Immunology's formatting requirements combine Nature Portfolio standards with immunology-specific demands around flow cytometry gating, antibody validation, and data presentation. The gating strategy requirement alone is responsible for a large share of revision requests at the journal, and it's entirely preventable 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.

In our pre-submission review work with manuscripts targeting Nature Immunology, four patterns generate the most consistent desk-rejection outcomes.

Missing or incomplete flow cytometry gating strategy. Nature Immunology's editorial office checks gating strategies before sending manuscripts to peer reviewers. Every flow cytometry experiment requires sequential gating shown from scatter gates through live/dead discrimination through lineage markers to the final analytical population. Papers with FACS data that only show the final analytical plots without showing how that population was defined are returned by the editorial office, not by reviewers. This is the single most preventable revision trigger at this journal. Include FMO controls for any marker where the gating boundary is not unambiguous.

Scope mismatch: specialist findings without broad immunology community relevance. Nature Immunology editors explicitly reject manuscripts on the basis of novelty and broad interest. 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 signals to Nature Immunology editors that the main story is not clearly organized. The journal's editorial guidance explicitly addresses this pattern: supplementary figures should contain data that is genuinely supplementary to the main story, not data that would have been figures 5 through 8 if the authors had not hit the display item limit. Editors use the main-to-supplementary ratio as a proxy for editorial confidence in the manuscript.

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