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Zmiz1-dependent Native Stem Cell Transcriptional Circuits in Normal and Malignant Immature T cells [RNA-seq]

GSE225125 Homo sapiens (human) RNA-seq (gene expression) 20 samples Submitted 2026/01/05 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 20 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Topic
Acute lymphoblastic leukemiaThis series is part of our curated briefing on it.
Samples
20 samples: 5 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
Native stem cell transcriptional circuits define cardinal features of high-risk leukemiaThe Journal of experimental medicine · 2025
Summary (written by the submitters)
The discovery of early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) was based on expression of stem cell genes that are characteristic of mouse ETP cells, the most primitive multipotent cells in the thymus.
Read the full summary ↓
Using complementary mouse and human genetic models and genome-wide expression and chromatin profiling integrated with 3D chromatin mapping, we show that the PIAS-like coactivator ZMIZ1 promotes immature T-ALL proliferation by recruiting the transcription factor MYB in feedforward circuits to cooperatively induce MYCN, MEF2C, and BCL2, which were recently associated with the high-risk bone marrow progenitor (BMP-like) subset. In the first experiment (Batch RS6) short hairpin RNAs shZMIZ1-13 (L13) and shZMIZ1-15 (L15) target the gene ZMIZ1 In the second experiment (Batch RS7) the gene MYB is knocked down.
Published in
Native stem cell transcriptional circuits define cardinal features of high-risk leukemia
Wang Q, Boccalatte F, Xu J et al. · The Journal of experimental medicine 2025 · PMID 39969525 · doi:10.1084/jem.20231349
This dataset
Open GSE225125 in finder → Find more human RNA-seq datasets → Acute lymphoblastic 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 GSE225125_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA934061 and SRA study SRP422103. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39969525) ↗
Study design
5 conditions, mostly with about 4 replicates each
Loucy shcontrol ×4 Loucy MYB KD ×4 Loucy hairpin nontargeting control ×4 Loucy ZMIZ1 hairpin knockdown -L13 ×4 Loucy ZMIZ1 hairpin knockdown -L15 ×4

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

How we read this: 5 replicated groups read from 20 sample titles; they account for 20 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
More Acute lymphoblastic leukemia datasets

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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.