Multi-Omics Data Downloads

A Molecular Atlas of Human Granulopoiesis

About This Dataset

This dataset contains transcriptome (mRNA), proteome, and microRNA (miRNA) profiles across seven defined stages of human neutrophil development:

Samples: 4 healthy donors + 1 biological replicate

Transcriptome (mRNA) Data

8,432 mRNA transcripts quantified across all maturation stages

QUANTIFIED COUNTS
Primary Count Data

Gene-level read counts quantified from RNA-seq. Ready for differential expression analysis with DESeq2 or edgeR.

CSV format

Download mrn_counts_raw.csv
LOG2 TRANSFORMED
Log2 Counts

Log2-transformed count data with pseudocount. Useful for visualization and fold-change calculations.

CSV format

Download mrn_counts_log2.csv
VSN NORMALIZED
VSN Stabilized Counts

Variance-stabilized count values. Optimal for statistical analysis and clustering across samples.

CSV format

Download mrn_counts_vsn.csv
TPM VALUES
TPM Normalized

Transcripts Per Million normalization. Best for comparing expression between genes within a sample.

CSV format

Download mrn_tpm_raw.csv
LOG2 TPM
Log2 TPM

Log2-transformed TPM values. Useful for visualizing expression patterns and calculating fold changes.

CSV format

Download mrn_tpm_lg2.csv
VSN NORMALIZED
VSN Stabilized TPM

Variance-stabilized TPM values. Best for multi-sample comparisons and integrative analysis.

CSV format

Download mrn_tpm_vsn.csv

Proteome Data

3,156 proteins quantified across all maturation stages

QUANTIFIED LFQ
Primary LFQ Intensities

Label-free quantification (LFQ) intensities from MaxQuant. Primary protein abundance values before normalization.

CSV format

Download pro_raw.csv
LOG2 TRANSFORMED
Log2 LFQ Intensities

Log2-transformed LFQ values. Standard format for protein differential expression analysis.

CSV format

Download pro_log2.csv
VSN NORMALIZED
VSN Stabilized

Variance-stabilized protein intensities. Optimal for multi-sample comparisons and clustering.

CSV format

Download pro_vsn.csv

microRNA (miRNA) Data

283 mature miRNA transcripts quantified across all maturation stages

QUANTIFIED COUNTS
Primary Count Data

Mature miRNA read counts from small RNA-seq. Starting point for miRNA analysis pipelines.

CSV format

Download mic_raw.csv
LOG2 TRANSFORMED
Log2 Counts

Log2-transformed miRNA counts. Suitable for differential expression and target prediction analysis.

CSV format

Download mic_log2.csv
VSN NORMALIZED
VSN Stabilized

Variance-stabilized miRNA expression. Best for integrative analysis with mRNA targets.

CSV format

Download mic_vsn.csv

Data Processing & Normalization Methods

Primary Quantified Data

Gene/protein-level quantification from standard pipelines (STAR/featureCounts for RNA-seq, MaxQuant for proteomics). These are not raw sequencing files but processed count matrices.

TPM (Transcripts Per Million)

Normalizes for gene length and sequencing depth. Best for comparing gene expression levels within a sample.

VSN (Variance Stabilizing Normalization)

Transforms data to stabilize variance across the entire range of expression values. Optimal for downstream statistical analysis and clustering.

Log2 Transformation

Logarithmic transformation (base 2) with pseudocount addition. Makes data more normally distributed and facilitates fold-change calculations.

Raw Sequencing Data Repositories

Gene Expression Omnibus (GEO) Public release pending

Accession: GSE294330

Contains raw RNA-seq and miRNA-seq data files

View on GEO
ProteomeXchange (PRIDE) Public release pending

Accession: PXD063208

Contains raw mass spectrometry proteomics data

View on PRIDE

How to Cite

If you use this data in your research, please cite:

Hesse S, Mao J, Hadziahmetovic A, et al. (2025) A molecular atlas of human granulopoiesis. Nature Communications (in submission)

Data availability:
• Transcriptome & miRNA: GEO GSE294330
• Proteome: PRIDE PXD063208
• Interactive platform: www.granulopoiesis.com