GEO series

Bulk mRNA-seq analysis of mouse hematopoietic stem and progenitor cells expressing wild-type and mutant H2B during myeloid and megakaryocyte/erythroid differentiation

GSE307414 Mus musculus (mouse) RNA-seq (gene expression) 15 samples Submitted 2026/03/02 Platform GPL34475

At a glance

RNA-seq (gene expression) · mouse · 15 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Mus musculus (mouse)
Samples: 15 samples
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: Nucleosome stability safeguards cell identity, stress resilience and healthy agingResearch square · 2025

Summary (written by the submitters)

Nucleosomes are the minimal repeating units of chromatin. Their dynamic assembly and disassembly underpins chromatin organization and genome regulation. However, how intrinsic nucleosome stability contributes to higher-level yet fundamental cellular and organismal properties—such as preservation of cell identity, lineage specification, stress resilience and healthy aging—remains unclear.

Read the full summary ↓

To address this, we tested the impact of intrinsic nucleosome instability across multiple cell, tissue and organismal models by introducing histone mutants that weaken histone–histone interactions. Despite no overt effects on global chromatin accessibility, DNA damage, steady-state proliferation or cell viability, nucleosome instability impaired lineage-specific gene expression programs, altered lineage specification and activated intrinsic inflammatory and stress pathways in a manner reminiscent of aging in mouse tissues and human cells. Consistently, in Caenorhabditis elegans and Drosophila melanogaster, nucleosome instability accelerated the onset of age-associated transcriptional alterations and functional decline in Caenorhabditis elegans and Drosophila melanogaster, and . At the cellular level, nucleosome instability also heightened cellular sensitivity vulnerability to exogenous perturbations—including environmental, epigenetic and mitotic stress—in human cells and Saccharomyces cerevisiaeyeast. These cross-species findings identify nucleosome stability as an evolutionarily conserved epigenetic safeguard that preserves cell identity and stress resilience, sustaining organismal function and longevity.

Published in

Nucleosome stability safeguards cell identity, stress resilience and healthy aging

Adams P, Tanaka H, McCauley B et al. · Research square 2025 · PMID 41333395 · doi:10.21203/rs.3.rs-7913970/v1

This dataset

Open GSE307414 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 GSE307414_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1321375 and SRA study SRP618141. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41333395) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 15 more — browse all 15 samples with per-sample file links →

Datasets on a similar topic

GSE308174 Bulk mRNA-seq analysis of mouse skeletal muscle, heart and liver expressing wild-type and mutant H2B 75 samples shares h2b, expressing, wild-type, mrna-seq
GSE278208 STING Mediates Increased Self-Renewal and Lineage Skewing in DNMT3A-Mutated Hematopoietic Stem/Progenitor Cells 40 samples shares hematopoietic, progenitor
GSE310548 Distinct contributions of Etv2+ and Flk1+ progenitors to endothelial, hematopoietic, and cardiac lineages [RNA-seq] 21 samples shares hematopoietic, progenitor
GSE294951 GABA produced by multiple bone marrow niche cell types regulate hematopoietic stem and progenitor cells 12 samples shares hematopoietic, progenitor
GSE272588 Multipotent progenitors with distinct origins, clonal lineage fates, transcriptomes, and surface markers yield two hematopoietic trees 605 samples shares hematopoietic, progenitor
GSE266188 Profiling of gene expression, histone marks, chromatin accessibility, and DNA methylation in myeloid progenitors expressing H3WT, H3K4M, H3K27M, or H3K4M/K27M for 2 weeks [CUT&Tag] 36 samples shares progenitor, expressing
GSE224160 Malaria pigment hemozoin-induced chromatin remodeling of mouse hematopoietic stem and progenitor cells, granulocyte-macrophage progenitors, and bone marrow monocytes 12 samples shares hematopoietic, progenitor
GSE230834 Impaired repopulating ability of Uhrf2-/- hematopoietic progenitor cells in mice. 12 samples shares hematopoietic, progenitor

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.