GEO series

Heterogeneity in hematopoietic stem cell enables adaptation to the aged microenvironment [scRNA-seq]

GSE327449 Mus musculus (mouse) Single-cell RNA-seq 12 samples Submitted 2026/07/21 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 12 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 12 samples: 12 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: Transcriptional heterogeneity predicts and enables clonal selection in ageing haematopoiesisResearch square · 2026

Summary (written by the submitters)

Aging reshapes hematopoietic stem cell (HSC) behavior, yet how pre-existing heterogeneity forecasts clonal performance in aged microenvironments remains unclear. Using cellular barcoding and single cell-RNA-seq to longitudinally sample shared sister-clones across hetero- and homochronic transplants in mice, we quantify (i) intra- and inter-cellular transcriptional heterogeneity in young and old HSC, (ii) differential self-renewal and clonal fitness of HSC in reconstituted

Read the full summary ↓

hematopoiesis, and (iii) clone-wise associations between pre-existing programs and fitness in aging contexts via predictive machine learning models. Old HSC exhibit greater heterogeneity and rates of generation of heterogeneity, driven by specific gene sets with known roles in HSC fitness. Old HSC exhibit higher self-renewal in old relative to young hosts, likely reflecting adaptation over life to the aged altered niche. Clones with higher fitness in aged mice are enriched for signatures of quiescence, genome integrity/DNA repair, and inflammaging when compared to lower-fitness clones before transplantation. Pre-existing heterogeneity predicts both higher clone fitness and higher self-renewal in the old hosts after transplantation, providing greater phenotypic variability for selection of adaptive clones. Together, these data argue that intrinsic aging encodes variable clonal ‘starting positions’ that interact with niche age to shape hematopoietic output. Our results contextualize recent clonal tracing studies in native hematopoiesis and aging—where lineage output is clonally restricted and age-expanded clones persist—and extend them by prospectively linking baseline HSC state variation to subsequent fitness under aged conditions. These findings nominate actionable, pre-transplant molecular predictors of clonal performance and suggest strategies to modulate aging programs to rebalance hematopoiesis.

Published in

Transcriptional heterogeneity predicts and enables clonal selection in ageing haematopoiesis

De Dominici M, Qian K, Chen X et al. · Research square 2026 · PMID 42396490 · doi:10.21203/rs.3.rs-10046174/v1

This dataset

Open GSE327449 in finder → Find more mouse 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 GSE327449_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 PRJNA1450963 and SRA study SRP690454. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42396490) ↗

Study design

12 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 12 sample titles: 12 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

GSM9657474 1_Ya, scRNAseq
GSM9657475 2_Ya, scRNAseq
GSM9657476 3_Ya, scRNAseq
GSM9657477 4_Oa, scRNAseq
GSM9657478 5_Oa, scRNAseq
GSM9657479 6_Oa, scRNAseq
GSM9657480 O1B, scRNA
GSM9657481 O2B, scRNA
GSM9657482 O3B, scRNA
GSM9657483 Y1B, scRNA
GSM9657484 Y2B, scRNA
GSM9657485 Y3B, scRNA

Datasets on a similar topic

GSE265909 yHSC and oHSC scRNAseq with oHSC AThi ATlo Index Sorting. Assessing the transcriptional changes associated with autophagy engagement in old hematopoietic stem cells at single cell resolution. [scRNA-Seq] 563 samples shares hematopoietic, scrna-seq, stem
GSE286398 Lysine-specific demethylase 1 regulates hematopoietic stem cell expansion and myeloid cell differentiation [scRNA-seq] 13 samples shares hematopoietic, scrna-seq, stem
GSE241770 ACSS2 mediates an epigenetic pathway to regulate maternal Beta-cell adaptation and progression of gestational diabetes (scRNA-Seq) 7899 samples shares adaptation, scrna-seq
GSE218178 Adaptation to an acid microenvironment promotes pancreatic cancer organoid growth and drug resistance 183 samples shares microenvironment, adaptation
GSE266509 A Bcl11a-driven mechanism maintaining hematopoietic stem cell functionality gives rise to dysfunction during aging [RNA-Seq] 52 samples shares hematopoietic, stem
GSE270016 Rejuvenation of aged oocyte through exposure to young follicular microenvironment 45 samples shares microenvironment, aged
GSE292146 Tractable mouse TNBC models capture the heterogeneous tumor immune microenvironment and adaptation to PD-L1 blockade 38 samples shares microenvironment, adaptation
GSE245315 Spatially restricted immune and microbiota-driven adaptation of the gut [scRNA-seq] 26 samples shares adaptation, scrna-seq

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.