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Hematopoiesis at single cell resolution spanning human development and maturation

GSE189161 Homo sapiens (human) Single-cell RNA-seq 26 samples Submitted 2024/07/29 Platform GPL18573
At a glance

Single-cell RNA-seq · human · 26 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Homo sapiens (human)
Samples
26 samples: 26 samples, each with a distinct title — no replicated groupsGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
The dynamics of hematopoiesis over the human lifespanNature methods · 2025
Summary (written by the submitters)
Hematopoiesis is a process of constitutive regeneration whereby hematopoietic stem and progenitor cells (HSPCs) constantly replenish mature blood cells. During maturation and aging, HSPCs alter their output to support the shifting demands of prenatal development and postnatal maturation both at homeostasis and in response to stress. How HSPC ontogeny changes throughout life is unknown; studies to date have largely focused on analysis of specific individual ages, particularly those done at single cell resolution.
Read the full summary ↓
Here, we performed single cell RNA-seq of human HSPCs from early prenatal development into mature adulthood, demonstrating dynamic remodeling of HSPC transcriptional states and differentiation trajectories over time. We identified age-specific gene expression patterns of lineage commitment throughout human life, and developed an approach for identifying, prospectively purifying, and functionally validating age-specific HSPC states. Together, our findings define the temporal evolution of hematopoiesis during human development and maturation, and uncover principles applicable to age-biased blood diseases.
Published in
The dynamics of hematopoiesis over the human lifespan
Li H, Côté P, Kuoch M et al. · Nature methods 2025 · PMID 39639169 · doi:10.1038/s41592-024-02495-0
This dataset
Open GSE189161 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE189161_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA781748. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39639169) ↗
Study design
26 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 26 sample titles: 26 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
Datasets on a similar topic

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.