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Fusion oncoproteins and cooperating mutations define disease phenotypes in NUP98-rearranged leukemia [RNA-seq]

GSE287297 Homo sapiens (human) RNA-seq (gene expression) 70 samples Submitted 2025/07/24 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 70 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)
Samples
70 samples: 18 conditions, mostly in duplicateGroups 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
Fusion oncoproteins and cooperating mutations define disease phenotypes in NUP98-rearranged leukemiaBlood · 2025
Summary (written by the submitters)
This series of expression data aims to investigate transcriptional profiling of cell lines or cord blood CD34+ cells transduced with various NUP98 fusion oncoproteins with or without cooperating alterations of RB1 loss or WT1 frameshift alterationss and menin inhibition with revumenib treatment.
Published in
Fusion oncoproteins and cooperating mutations define disease phenotypes in NUP98-rearranged leukemia
Umeda M, Hiltenbrand R, Michmerhuizen NL et al. · Blood 2025 · PMID 40700635 · doi:10.1182/blood.2025028993
This dataset
Open GSE287297 in finder → Find more human 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 GSE287297_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 PRJNA1212059 and SRA study SRP558126. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40700635) ↗
Study design
18 conditions, mostly in duplicate
KDM5A and Cas9 + gRNA (RB1-gRNA1) + DMSO-trea… ×3 KDM5A and Cas9 + gRNA (WT1-gRNA1) + DMSO-trea… ×3 KDM5A and Cas9 + gRNA (RB1-gRNA1) + Revumenib… ×3 KDM5A and Cas9 + gRNA (WT1-gRNA1) + Revumenib… ×3 KDM5A and Cas9 + gRNA (AAVS) + DMSO-treatment… ×2 KDM5A and Cas9 + gRNA (AAVS) + Revumenib (1 u… ×2 cord blood CD34+ cell with empty vector contr… ×2 NSD1 rep1 at day ×2 +40 more

Supports a between-group comparison across 40 samples.

How we read this: 18 replicated groups read from 70 sample titles; they account for 40 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

+ 30 more — browse all 70 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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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.