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Intracellular iron homeostasis-regulated epigenetic reprogramming contributes to -7/del(7q) leukemia

GSE294258 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 71 samples Submitted 2026/04/21 Platform GPL24247Platform GPL34328Platform GPL33944
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 71 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
71 samples: 53 distinct titles, 12 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.
Summary (written by the submitters)
Chromosome copy number variations are poorly understood drivers of human malignancies. -7/del(7q) is common in acute myeloid leukemia, confers a poor prognosis, and is thought to harbor several tumor suppressors. Previously, we identified the histone methyltransferase KMT2C as a tumor suppressor in this region. Here, through a differentiation CRISPR screen in hematopoietic stem and progenitor cells, we find that the mitochondrial iron transporter ABCB8 is essential for their differentiation.
Read the full summary ↓
ABCB8 deficiency accelerates leukemogenesis in vivo and disrupts iron homeostasis, reducing cytoplasmic iron availability and impairing iron-dependent enzymes, including the histone demethylase KDM6A. Consequently, ABCB8 loss elevates H3K27me3 levels, repressing differentiation genes in an iron- and KDM6A-dependent manner. Notably, ABCB8 and KMT2C, neighboring genes on 7q, cooperatively regulate H3K27me3 to suppress leukemogenesis. Our findings reveal ABCB8 as a tumor suppressor in -7/del(7q) acute myeloid leukemia and uncover an epigenetic collaboration between neighboring tumor suppressors, driven by iron-mediated chromatin remodeling.
This dataset
Open GSE294258 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 GSE294258_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 PRJNA1248888 and SRA study SRP577711. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
53 distinct titles, 12 of them repeated
H3K27me3 CUT&Tag Seq of mouse HSPCs with shRen ×3 H3K27me3 CUT&Tag Seq of mouse HSPCs with shKm… ×3 H3K27me3 CUT&Tag Seq of mouse HSPCs with shAb… ×3 H3K27me3 CUT&Tag Seq of mouse HSPCs with shAb… ×3 sorted_H3K27me3_shRen ×3 sorted_H3K27me3_shAbcb8 ×3 mouse HSPCs with shRen rep1, ×2 mouse HSPCs with shRen rep2, ×2 +4 more

Supports a case/control comparison: 6 samples read as cases, 8 as controls.

How we read this: Read from 71 sample titles: 53 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

+ 31 more — browse all 71 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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