GEO series

Distinct roles for NF-κB in hematopoietic stem cells and the bone marrow milieu in promoting hematopoietic aging

GSE264569 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 24 samples Submitted 2025/08/25 Platform GPL19057

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 24 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Mus musculus (mouse)
Samples: 24 samples: 8 conditions, mostly in triplicateGroups 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: Distinct roles for NF-κB in hematopoietic stem cells and the bone marrow milieu in promoting hematopoietic agingCell reports · 2025

Summary (written by the submitters)

Hematopoietic aging is characterized by chronic inflammation associated with myeloid bias, hematopoietic stem cell (HSC) accumulation, and functional HSC impairment. Yet it remains unclear how inflammation promotes aging phenotypes. Nuclear factor κB (NF-κB) both responds to and directs inflammation, and we present an experimental model of elevated NF-κB activity ("inhibitor of κB deficient" [IκB-]) to dissect its role in hematopoietic aging phenotypes.

Read the full summary ↓

We find that while elevated NF-κB activity is not sufficient for HSC accumulation, HSC-autonomous NF-κB activity impairs their functionality, leading to reduced bone marrow reconstitution. In contrast, myeloid bias is driven by the IκB- proinflammatory bone marrow milieu, as observed functionally, epigenomically, and transcriptomically. A single-cell RNA sequencing (scRNA-seq) HSPC labeling framework enables comparisons with aged murine and human HSC datasets, documenting an association between HSC-intrinsic NF-κB activity and quiescence but not myeloid bias. These findings delineate separate regulatory mechanisms that underlie the three hallmarks of hematopoietic aging, suggesting that they are specifically and independently therapeutically targetable.

Published in

Distinct roles for NF-κB in hematopoietic stem cells and the bone marrow milieu in promoting hematopoietic aging

Chia JJ, Singh A, Lin YS et al. · Cell reports 2025 · PMID 40875292 · doi:10.1016/j.celrep.2025.116193

This dataset

Open GSE264569 in finder → Find more mouse ChIP / ATAC / CUT&Tag 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 GSE264569_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 peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1103170 and SRA study SRP503336. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40875292) ↗

Study design

8 conditions, mostly in triplicate

WT recip, HSC, ×3 WT recip, MPP2, ×3 WT recip, MPP3, ×3 WT recip, MPP4, ×3 IκB– recip, HSC, ×3 IκB– recip, MPP2, ×3 IκB– recip, MPP3, ×3 IκB– recip, MPP4, ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 of them. 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

GSM8222798 WT recip, HSC, rep1 WT recip, HSC,
GSM8222799 WT recip, HSC, rep2 WT recip, HSC,
GSM8222800 WT recip, HSC, rep3 WT recip, HSC,
GSM8222801 WT recip, MPP2, rep1 WT recip, MPP2,
GSM8222802 WT recip, MPP2, rep2 WT recip, MPP2,
GSM8222803 WT recip, MPP2, rep3 WT recip, MPP2,
GSM8222804 WT recip, MPP3, rep1 WT recip, MPP3,
GSM8222805 WT recip, MPP3, rep2 WT recip, MPP3,
GSM8222806 WT recip, MPP3, rep3 WT recip, MPP3,
GSM8222807 WT recip, MPP4, rep1 WT recip, MPP4,
GSM8222808 WT recip, MPP4, rep2 WT recip, MPP4,
GSM8222809 WT recip, MPP4, rep3 WT recip, MPP4,
GSM8222810 IκB– recip, HSC, rep1 IκB– recip, HSC,
GSM8222811 IκB– recip, HSC, rep2 IκB– recip, HSC,
GSM8222812 IκB– recip, HSC, rep3 IκB– recip, HSC,
GSM8222813 IκB– recip, MPP2, rep1 IκB– recip, MPP2,
GSM8222814 IκB– recip, MPP2, rep2 IκB– recip, MPP2,
GSM8222815 IκB– recip, MPP2, rep3 IκB– recip, MPP2,
GSM8222816 IκB– recip, MPP3, rep1 IκB– recip, MPP3,
GSM8222817 IκB– recip, MPP3, rep2 IκB– recip, MPP3,
GSM8222818 IκB– recip, MPP3, rep3 IκB– recip, MPP3,
GSM8222819 IκB– recip, MPP4, rep1 IκB– recip, MPP4,
GSM8222820 IκB– recip, MPP4, rep2 IκB– recip, MPP4,
GSM8222821 IκB– recip, MPP4, rep3 IκB– recip, MPP4,

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