A Molecular Atlas of Human Granulopoiesis

Comprehensive multi-omics analysis across 7 developmental stages

Hesse, Klein et al., Nature Communications (under revision)

Major Revision Updated: October 2025

Atlas Overview: feature space for each development stage

mRNA
8,432

mRNA Transcripts

Proteins
3,156

Proteins

miRNAs
283

miRNAs

Stages
7 stages

Myeloblast → Neutrophil granulocyte

Interactive Data Explorer

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Paper Figures

Interactive versions with underlying data and code

Figure 2: Multi-omics Overview
Multi-omics Overview

Transcriptome, proteome, and miRNome landscapes across 7 stages

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Figure 3: Longitudinal Trajectories
Longitudinal Trajectories

Feature trajectories and molecular pathways of granulopoiesis

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Figure 4: miRNA Governance
miRNA Governance

miRNA-mRNA interaction networks and regulatory effects

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Figure 5: TF & lncRNA Analysis
TF & lncRNA Analysis

Transcription factors, lncRNAs and omics-shifts

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Supplementary

Supplementary Figures

Additional analyses, controls and extended data

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📄 Preprint

Read the Full Manuscript

The complete preprint is available on Research Square

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Download Data

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All data formats • VSN, TPM, Log2 normalized • Direct downloads

Transcriptome

8,432 genes • All formats

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Proteome

3,156 proteins • All formats

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miRNome

283 miRNAs • All formats

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Raw Data Repository

RNA-seq & miRNA-seq:

Deposited to GEO: GSE294330

Reviewer token available upon request

Proteomics:

Deposited to PRIDE: PXD063208

Reviewer access provided

Analysis Scripts

Complete reproducible analysis pipeline

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📊 21 Complete Analysis Reports Available
  • Data preparation (RNA-seq, Proteomics, miRNA)
  • Differential expression analysis
  • WGCNA and timeOmics trajectory analysis
  • miRNA-mRNA interaction analysis
  • Transcription factor analysis
  • Enrichment analyses
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Analysis Scripts & Code

Complete reproducible analysis pipeline

Core Analyses
  • RNA-seq processing (STAR)
  • Proteomics (MaxQuant)
  • miRNA analysis
  • Differential expression
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Integration
  • WGCNA trajectories
  • timeOmics
  • miRNA-mRNA networks
  • Φ-Space integration
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Validation
  • Sex analysis (NEW)
  • Public data validation
  • COVID-19 integration
  • Statistical reports
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Citation

Under Revision Nature Communications

Nature Communications (under revision)

DOI: Pending publication

Data Availability
All data supporting this study are available at www.granulopoiesis.com. Raw sequencing data: GEO GSE294330, PRIDE PXD063208.