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Chromation accessibility profiles of cKit positive bone marrow cells from six genotype mice - WT, Idh1R132, Npm1c, Flt3ITD, Idh1R132+Npm1c, and Idh1R132+Flt3ITD

GSE215367 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 47 samples Submitted 2025/04/30 Platform GPL21103
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 47 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
47 samples: 12 conditions, mostly with about 4 replicates eachGroups 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
Mutant IDH1 cooperates with NPM1c or FLT3(ITD) to drive distinct myeloid diseases and molecular outcomesProceedings of the National Academy of Sciences of the United States of America · 2025
Summary (written by the submitters)
Here we show that the combination of Idh1R132 plus Npm1c mutations cooperatively induced overt AML in vivo, using genetically engineered mouse model. In contrast, the combination of Idh1R132 plus Flt3ITD led to myeloid proliferation disease, but not AML. The mice harboring both of Idh1R132 and Npm1c mutations got fatal (median survival, 254 days) due to AML, which demonstrated rapid lethality on recipient mice in secondary transplantation experiments.
Read the full summary ↓
We analyzed cKit-positive bone marrow cells from six genotype mice - WT, Idh1R132, Npm1c, Flt3ITD, Idh1R132+Npm1c, and Idh1R132+Flt3ITD. We isolated cKit positive BM cells from the mice of the two different ages (3 and 6 months old), and subjected to RNA-seq, bisulfite-seq, and ATAC-seq.
Published in
Mutant IDH1 cooperates with NPM1c or FLT3(ITD) to drive distinct myeloid diseases and molecular outcomes
Sakamoto T, Leca J, Zhang X et al. · Proceedings of the National Academy of Sciences of the United States of America 2025 · PMID 40377995 · doi:10.1073/pnas.2415779122
This dataset
Open GSE215367 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 GSE215367_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 PRJNA889925 and SRA study SRP402286. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40377995) ↗
Study design
12 conditions, mostly with about 4 replicates each
3mo WT ×4 3mo IDH1 ×4 3mo IDH1NPM1 ×4 3mo FLT3 ×4 3mo IDH1FLT3 ×4 6mo WT ×4 6mo IDH1 ×4 6mo NPM1 ×4 +4 more

Supports a between-group comparison across 47 samples.

How we read this: 12 replicated groups read from 47 sample titles; they account for 47 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

+ 7 more — browse all 47 samples with per-sample file links →

Datasets on a similar topic

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