Transcriptional and epigenetic rewiring by the NUP98::KDM5A fusion oncoprotein directly activates CDK12 (Cut&Tag)
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 20 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
- 20 samples: 6 conditions, mostly in triplicateGroups 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
- Transcriptional and epigenetic rewiring by the NUP98::KDM5A fusion oncoprotein directly activates CDK12Nature communications · 2025
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE255802_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1076553 and SRA study SRP489766. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 6 replicated groups read from 20 sample titles; they account for 18 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.
- GSM8080321 cutntag_DMSO_H3K27ac_1 cutntag_DMSO_H3K27ac
- GSM8080322 cutntag_DMSO_H3K27ac_2 cutntag_DMSO_H3K27ac
- GSM8080323 cutntag_DMSO_H3K27ac_3 cutntag_DMSO_H3K27ac
- GSM8080324 cutntag_DMSO_H3K4me3_1 cutntag_DMSO_H3K4me3
- GSM8080325 cutntag_DMSO_H3K4me3_2 cutntag_DMSO_H3K4me3
- GSM8080326 cutntag_DMSO_H3K4me3_3 cutntag_DMSO_H3K4me3
- GSM8080327 cutntag_DMSO_IgG_1
- GSM8080328 cutntag_H3K27ac_1 cutntag_H3K27ac
- GSM8080329 cutntag_H3K4me3_1 cutntag_H3K4me3
- GSM8080330 cutntag_IgG_1
- GSM8080331 cutntag_H3K27ac_2 cutntag_H3K27ac
- GSM8080332 cutntag_H3K4me3_2 cutntag_H3K4me3
- GSM8080333 cutntag_H3K27ac_3 cutntag_H3K27ac
- GSM8080334 cutntag_H3K4me3_3 cutntag_H3K4me3
- GSM8080335 cutntag_dTAG13_H3K27ac_1 cutntag_dTAG13_H3K27ac
- GSM8080336 cutntag_dTAG13_H3K27ac_2 cutntag_dTAG13_H3K27ac
- GSM8080337 cutntag_dTAG13_H3K27ac_3 cutntag_dTAG13_H3K27ac
- GSM8080338 cutntag_dTAG13_H3K4me3_1 cutntag_dTAG13_H3K4me3
- GSM8080339 cutntag_dTAG13_H3K4me3_2 cutntag_dTAG13_H3K4me3
- GSM8080340 cutntag_dTAG13_H3K4me3_3 cutntag_dTAG13_H3K4me3
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- GSE270185 Repurposing CD19-directed immunotherapies for pediatric t(8;21) acute myeloid leukemia 249 samples same disease briefing
- GSE137574 Kevetrin induces apoptosis in TP53 wild-type and mutant acute myeloid leukemia cells 24 samples same disease briefing
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- GSE122515 Bonn Dataset 3 of meta-analysis on AML classification, RNAseq dataset 0 samples same disease briefing
- GSE269258 HoxBlinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98 fusion transformed leukemia 61 samples shares nup98
- GSE283531 MOZ and HBO1 Histone Acetyltransferase Complexes Are Molecular Dependencies and Therapeutic Targets in NUP98-Rearranged Acute Myeloid Leukemia [RNA-Seq] 54 samples shares nup98
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.