Scientific manuscript

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Scientific Manuscript Preparation

Document Structure for High-Impact Journals

Title

• Concise (<15 words for Nature, <20 for Blood)
• Include key finding and system/disease
• Avoid jargon and abbreviations

Abstract (Structured for Blood/Clinical Journals)

**Background:** One sentence on knowledge gap.
**Methods:** Key approaches, patient cohort size, techniques.
**Results:** Primary findings with statistics (P values, CIs).
**Conclusions:** Clinical/translational significance.

Introduction (~500-800 words)

1. Paragraph 1: Broad context, disease burden, clinical relevance
2. Paragraph 2: Current knowledge, key mechanisms
3. Paragraph 3: Knowledge gap, unanswered questions
4. Paragraph 4: Study aims, hypothesis, approach overview

Methods (Detailed, Reproducible)

**Patient Cohort and Samples**
- IRB approval number, consent process
- Inclusion/exclusion criteria
- Sample processing, storage conditions

**Single-Cell RNA Sequencing**
- Library preparation (10x Genomics Chromium 3' v3.1)
- Sequencing platform, read depth
- Quality metrics (cells/sample, genes/cell, % mitochondrial)

**Computational Analysis**
- Software versions (Scanpy 1.9.x, scvi-tools 0.20.x)
- QC thresholds (min genes, max %MT)
- Integration method (TotalVI, Harmony)
- Clustering parameters (resolution, n_neighbors)
- Differential expression (Wilcoxon, FDR < 0.05, |log2FC| > 1)

**Statistical Analysis**
- Software (R 4.3.x, Python 3.11)
- Tests used with justification
- Multiple testing correction method
- Power analysis if applicable

Results (~2000-3000 words)

• Lead each paragraph with key finding
• Reference figures in order (Figure 1A-C...)
• Report exact P values (P = 0.003, not P < 0.05)
• Include confidence intervals where relevant
• Avoid interpretation; save for Discussion

Discussion (~1500-2000 words)

**Paragraph 1**: Summarize key findings, relate to hypothesis

**Paragraph 2-4**: Compare to existing literature
- "Consistent with [Author et al.], we found..."
- "In contrast to [Study], our analysis revealed..."
- Mechanistic interpretation

**Paragraph 5**: Translational/Clinical implications
- Therapeutic targets
- Biomarkers
- Patient stratification

**Paragraph 6**: Limitations
- Sample size, cohort characteristics
- Technical limitations
- Generalizability

**Paragraph 7**: Future directions and conclusion

Statistical Reporting Standards

Continuous Variables

• Mean ± SD (normal) or Median [IQR] (non-normal)
• Report normality test used

Categorical Variables

• N (%) with comparison test

P Values

• Report exact values (P = 0.023)
• For very small: P < 0.0001
• Always report test used

Sample Sizes

• "n = X patients" or "n = X cells"
• Report for each comparison group

Figure Legends Template

**Figure 1. Title describes main finding**
(A) Brief description of panel A. Statistical test, P value.
(B) Description including axis labels if not obvious.
(C-D) Can combine similar panels.
Scale bars: X μm. Error bars: mean ± SEM. *P < 0.05, **P < 0.01, ***P < 0.001.
n = X biological replicates from Y independent experiments.

Reference Formatting

Blood Journal (Vancouver)

1. Smith JA, Jones BC. Title of article. Blood. 2024;143(5):567-578.

Nature (Author-Year)

Smith, J.A. & Jones, B.C. Title of article. Nature 620, 567–578 (2024).

Journal-Specific Requirements

Blood (ASH)

• Word limit: 4000 (full article)
• Figures: 7 max
• References: 60 max
• Structured abstract: 250 words

Nature

• Word limit: ~3000 (Article)
• Main text figures: 6-8
• Methods: no limit, separate section
• Extended Data for supplementary figures

Cell

• Word limit: 7000 (Article)
• STAR Methods format
• Graphical abstract required

HIPAA Compliance Reminders

• No patient identifiers in any form
• Use Specimen IDs, not patient names/MRNs
• Aggregate data for small groups (n < 5)
• IRB approval statement required
• Data availability statement (GEO accession for sequencing)

Writing Style

• Active voice preferred
• Past tense for results ("We found...")
• Present tense for established facts
• Avoid "interesting," "significant" (unless statistical)
• Be specific: "83.9-fold increase" not "marked increase"

See references/journal_templates.md for specific formats. See references/statistical_tests.md for test selection guide.

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