Transcriptional and epigenetic rewiring by the NUP98::KDM5A fusion oncoprotein directly activates CDK12 (RNA-Seq)
RNA-seq (gene expression) · mouse · 16 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
- Mus musculus (mouse)
- Samples
- 16 samples: 4 × quant_BSJ_4h vs 4 × quant_DMSO vs 4 × quant_dTAG_24h vs 4 × quant_dTAG_8hGroups 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 GSE255807_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: 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 PRJNA1076561 and SRA study SRP489770. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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.
- GSM8080362 quant_BSJ_4h_1 quant_BSJ_4h
- GSM8080363 quant_BSJ_4h_2 quant_BSJ_4h
- GSM8080364 quant_BSJ_4h_3 quant_BSJ_4h
- GSM8080365 quant_BSJ_4h_4 quant_BSJ_4h
- GSM8080366 quant_DMSO_1 quant_DMSO
- GSM8080367 quant_DMSO_2 quant_DMSO
- GSM8080368 quant_DMSO_3 quant_DMSO
- GSM8080369 quant_DMSO_4 quant_DMSO
- GSM8080370 quant_dTAG_24h_1 quant_dTAG_24h
- GSM8080371 quant_dTAG_24h_2 quant_dTAG_24h
- GSM8080372 quant_dTAG_24h_3 quant_dTAG_24h
- GSM8080373 quant_dTAG_24h_4 quant_dTAG_24h
- GSM8080374 quant_dTAG_8h_1 quant_dTAG_8h
- GSM8080375 quant_dTAG_8h_2 quant_dTAG_8h
- GSM8080376 quant_dTAG_8h_3 quant_dTAG_8h
- GSM8080377 quant_dTAG_8h_4 quant_dTAG_8h
- GSE255805 Transcriptional and epigenetic rewiring by the NUP98::KDM5A fusion oncoprotein directly activates CDK12 (nascent RNA-Seq) 6 samples shares nup98, kdm5a, cdk12, oncoprotein, epigenetic, activates, rewiring, directly
- GSE278066 Transcriptional and epigenetic rewiring by the NUP98::KDM5A fusion oncoprotein directly activates CDK12 (ATAC-seq) 3 samples shares nup98, kdm5a, cdk12, oncoprotein, epigenetic, activates, rewiring, directly
- GSE254390 CDK12 Loss Promotes Prostate Cancer Development While Exposing Vulnerabilities to Paralog-Based Synthetic Lethality 20 samples shares cdk12
- GSE274479 Non-Canonical PRC1.1 is required for the activity of Menin-MLL1 Inhibitors in NUP98-Rearranged AML [RNA-seq] 15 samples shares nup98
- GSE254388 CDK12 Loss Promotes Prostate Cancer Development While Exposing Vulnerabilities to Paralog-Based Synthetic Lethality [RNA-Seq] 14 samples shares cdk12
- GSE283088 CDK12/13 inactivation triggers STING-mediated antitumor immunity in preclinical models [RNA-seq] 12 samples shares cdk12
- GSE279389 Loss of NOL10 leads to impaired disease progression of NUP98::DDX10 leukemia 9 samples shares nup98
- GSE282047 Clec12a is required for the pathogenesis of NUP98::NSD1 AML 6 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.