GEO series

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

GSE215368 Mus musculus (mouse) DNA methylation 52 samples Submitted 2025/04/30 Platform GPL21103

At a glance

DNA methylation · mouse · 52 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Mus musculus (mouse)
Samples: 52 samples: 12 conditions, mostly with about 5 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 GSE215368 in finder → Find more mouse methylation 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 GSE215368_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 PRJNA889927 and SRA study SRP402285. 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 5 replicates each

6mo WT OxBS ×5 6mo IDH1 OxBS ×5 6mo NPM1 OxBS ×5 6mo IDH1NPM1 OxBS ×5 6mo FLT3 OxBS ×5 6mo IDH1FLT3 OxBS ×5 3mo WT OxBS ×4 3mo IDH1 OxBS ×4 +4 more

Supports a between-group comparison across 52 samples.

How we read this: 12 replicated groups read from 52 sample titles; they account for 52 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

GSM6634462 3mo WT OxBS Rep1 3mo WT OxBS
GSM6634463 3mo WT OxBS Rep2 3mo WT OxBS
GSM6634464 3mo WT OxBS Rep3 3mo WT OxBS
GSM6634465 3mo WT OxBS Rep4 3mo WT OxBS
GSM6634466 3mo IDH1 OxBS Rep1 3mo IDH1 OxBS
GSM6634467 3mo IDH1 OxBS Rep2 3mo IDH1 OxBS
GSM6634468 3mo IDH1 OxBS Rep3 3mo IDH1 OxBS
GSM6634469 3mo IDH1 OxBS Rep4 3mo IDH1 OxBS
GSM6634470 3mo NPM1 OxBS Rep1 3mo NPM1 OxBS
GSM6634471 3mo NPM1 OxBS Rep2 3mo NPM1 OxBS
GSM6634472 3mo NPM1 OxBS Rep3 3mo NPM1 OxBS
GSM6634473 3mo NPM1 OxBS Rep4 3mo NPM1 OxBS
GSM6634474 3mo IDH1NPM1 OxBS Rep1 3mo IDH1NPM1 OxBS
GSM6634475 3mo IDH1NPM1 OxBS Rep3 3mo IDH1NPM1 OxBS
GSM6634476 3mo IDH1NPM1 OxBS Rep4 3mo IDH1NPM1 OxBS
GSM6634477 3mo FLT3 OxBS Rep1 3mo FLT3 OxBS
GSM6634478 3mo FLT3 OxBS Rep2 3mo FLT3 OxBS
GSM6634479 3mo FLT3 OxBS Rep3 3mo FLT3 OxBS
GSM6634480 3mo FLT3 OxBS Rep4 3mo FLT3 OxBS
GSM6634481 3mo IDH1FLT3 OxBS Rep1 3mo IDH1FLT3 OxBS
GSM6634482 3mo IDH1FLT3 OxBS Rep2 3mo IDH1FLT3 OxBS
GSM6634483 3mo IDH1FLT3 OxBS Rep4 3mo IDH1FLT3 OxBS
GSM6634484 6mo WT OxBS Rep1 6mo WT OxBS
GSM6634485 6mo WT OxBS Rep2 6mo WT OxBS
GSM6634486 6mo WT OxBS Rep3 6mo WT OxBS
GSM6634487 6mo WT OxBS Rep4 6mo WT OxBS
GSM6634488 6mo WT OxBS Rep5 6mo WT OxBS
GSM6634489 6mo IDH1 OxBS Rep1 6mo IDH1 OxBS
GSM6634490 6mo IDH1 OxBS Rep2 6mo IDH1 OxBS
GSM6634491 6mo IDH1 OxBS Rep3 6mo IDH1 OxBS
GSM6634492 6mo IDH1 OxBS Rep4 6mo IDH1 OxBS
GSM6634493 6mo IDH1 OxBS Rep5 6mo IDH1 OxBS
GSM6634494 6mo NPM1 OxBS Rep1 6mo NPM1 OxBS
GSM6634495 6mo NPM1 OxBS Rep2 6mo NPM1 OxBS
GSM6634496 6mo NPM1 OxBS Rep3 6mo NPM1 OxBS
GSM6634497 6mo NPM1 OxBS Rep4 6mo NPM1 OxBS
GSM6634498 6mo NPM1 OxBS Rep5 6mo NPM1 OxBS
GSM6634499 6mo IDH1NPM1 OxBS Rep1 6mo IDH1NPM1 OxBS
GSM6634500 6mo IDH1NPM1 OxBS Rep2 6mo IDH1NPM1 OxBS
GSM6634501 6mo IDH1NPM1 OxBS Rep3 6mo IDH1NPM1 OxBS

+ 12 more — browse all 52 samples with per-sample file links →

Datasets on a similar topic

GSE215369 Gene expression profiles of cKit positive bone marrow cells from six genotype mice - WT, Idh1R132, Npm1c, Flt3ITD, Idh1R132+Npm1c, and Idh1R132+Flt3ITD 54 samples shares idh1r132, flt3itd, npm1c, profiles, positive, genotype, marrow
GSE215367 Chromation accessibility profiles of cKit positive bone marrow cells from six genotype mice - WT, Idh1R132, Npm1c, Flt3ITD, Idh1R132+Npm1c, and Idh1R132+Flt3ITD 47 samples shares idh1r132, flt3itd, npm1c, profiles, positive, genotype, marrow
GSE264700 RNA sequencing of NPM1cA/SMC+/- mouse myeloid sarcoma and whole bone marrow 16 samples shares npm1c, marrow
GSE166226 Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates 615 samples shares methylation
GSE166225 Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates [RNA-seq] 288 samples shares methylation
GSE225173 Predicting age in single cells and low coverage DNA methylation data 250 samples shares methylation
GSE296994 H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation 174 samples shares methylation
GSE292524 Intrinsic de novo DNA methylation in early embryos enables the generation of semi-cloned mice from methylation-deficient androgenetic haploid stem cells 174 samples shares methylation

Search all mouse methylation 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.