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Transposable Elements Shape Stemness in Normal and Leukemic Hematopoiesis

GSE234237 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 215 samples Submitted 2026/01/15 Platform GPL24676Platform GPL20301
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 215 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
Homo sapiens (human)
Topic
Acute myeloid leukemiaThis series is part of our curated briefing on it.
Samples
215 samples: 191 distinct titles, 3 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
Transposable elements shape stemness in normal and leukemic hematopoiesisNature genetics · 2026
Summary (written by the submitters)
Despite most acute myeloid leukemia (AML) patients achieving complete remission after induction chemotherapy, two thirds of patients will relapse with fatal disease within 5 years. AML is organized as a cellular hierarchy sustained by leukemia stem cells (LSC) at the apex, with LSC properties directly linked to tumor progression, therapy failure and disease relapse.
Read the full summary ↓
Despite the central role of LSC in poor patient outcomes, little is known of the genetic determinants of their stemness properties. Although much AML research focuses on mutational processes and their impact on gene expression programs, the genetic determinants of cell state properties including stemness expand beyond mutations, relying on the genetic architecture captured in the chromatin of each cell. As LSCs share many functional and molecular properties with normal hematopoietic stem cells (HSC), we identified genetic determinants of primitive populations enriched for LSCs and HSCs in comparison with their downstream mature progeny by investigating their chromatin accessibility. Our work reveals how distinct transposable element families are used in primitive versus mature populations, functioning as docking sites for stem cell-associated regulators of genome topology or lineage-specific transcription factors in primitive and mature populations, respectively. We further show how transposable element families accessible in LSCs define docking sites for several oncogenic drivers in AML, including LYL1. Using chromatin accessibility profiles from a cohort of AML patients, we further show the clinical utility of our transposable element accessibility-based LSCTE121 scoring scheme to identify patients with high rates of relapse. Collectively, our work reveals how different accessible transposable element families serve as genetic determinants of stemness properties in normal and leukemic hematopoietic stem cells.
Published in
Transposable elements shape stemness in normal and leukemic hematopoiesis
Grillo G, Nadorp B, Qamra A et al. · Nature genetics 2026 · PMID 42082719 · doi:10.1038/s41588-026-02585-z
This dataset
Open GSE234237 in finder → Find more human ChIP / ATAC / CUT&Tag datasets → Acute myeloid leukemia landscape →
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 GSE234237_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 PRJNA980608 and SRA study SRP497905. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42082719) ↗
Study design
191 distinct titles, 3 of them repeated
PB bulk, ×21 OCI-AML22 - C ×3 OCI-AML22 - LTR12C ×3

How we read this: Read from 215 sample titles: 191 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

+ 175 more — browse all 215 samples with per-sample file links →

More Acute myeloid leukemia datasets

Search all human ChIP / ATAC / CUT&Tag datasets in GEO →

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