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Age-like Methylation Changes of HSCs in Gadd45b knock-out mice

GSE276335 Mus musculus (mouse) DNA methylation 29 samples Submitted 2026/05/15 Platform GPL24247
At a glance

DNA methylation · mouse · 29 samples

What it is
DNA methylationChemical marks on DNA that help switch genes on or off.
Organism
Mus musculus (mouse)
Samples
29 samples: 25 distinct titles, 2 of them repeatedGroups 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
Age-Like Methylation Changes of HSCs in GADD45B Knockout Mice Define Methylation Sites Associated With Loss of FunctionAging cell · 2026
Summary (written by the submitters)
Age-related functional decline of hematopoietic stem cells (HSC) contributes to the decline of the hematopoietic system. Growth Arrest and DNA Damage-inducible proteins (Gadd45a, Gadd45b, and Gadd45g) are robustly expressed early in HSC activation and are known to be important for DNA damage response. Gadd45b has also been shown to promote removal of 5-methylcytosine at specific loci.
Read the full summary ↓
Given that both DNA methylation (DNAm) alterations and DNA damage have been associated with HSC aging, we sought to examine the role of Gadd45b in HSCs. To examine if Gadd45b is critical for regulating DNAm in HSCs, we performed whole genome bisulfite sequence and RNA sequencing on wild-type (WT) and Gadd45b knock-out (KO) HSCs isolated from young and old mice. Global DNAm of young KO showed increased DNAm compared to young WT, and the DNAm profiles were more similar to old HSCs, from either WT and KO, than to young WT. We examined the DNAm changes common between the Gadd45b KO (YKOvsYWT) or WT aging (OWTvsYWT). 52.5% of differentially methylated cytosines (DMCs) in YKO were also seen in normal aging, and analysis of genes with promoters near these overlapping DMCs are enriched for pathways related to immune response and development processes. We compared the expression of genes with DMCs in the promoter regions, but DMCs did not strongly correspond with transcriptional alterations. To test if these overlapping DNAm changes in young KO mice primed HSCs towards aging phenotypes, we evaluated the composition of peripheral blood and bone marrow in KO, and performed functional evaluation experiments. We found no significant differences between young KO and WT HSCs suggesting these overlapping DMCs do not contribute to aging phenotypes, reducing the potential DNAm changes contributing to aging HSC phenotypes.
Published in
Age-Like Methylation Changes of HSCs in GADD45B Knockout Mice Define Methylation Sites Associated With Loss of Function
Kuribayashi W, Tanaka-Yano M, Park B et al. · Aging cell 2026 · PMID 41860580 · doi:10.1111/acel.70453
This dataset
Open GSE276335 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 GSE276335_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: Look for beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA1156683 and SRA study SRP530489. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41860580) ↗
Study design
25 distinct titles, 2 of them repeated
45b_Young_HSC ×3 45b_Old_HSC ×3

How we read this: Read from 29 sample titles: 25 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
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