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Targeted Degradation of CDK9 Potently Disrupts MYC Network

GSE263153 Homo sapiens (human) RNA-seq (gene expression) 91 samples Submitted 2025/05/07 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 91 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
91 samples: 23 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
Targeted degradation of CDK9 potently disrupts the MYC-regulated networkCell chemical biology · 2025
Summary (written by the submitters)
Cyclin-dependent kinase 9 (CDK9) coordinates signaling events that regulate RNA polymerase II (Pol II) pause-release states. It is an important co-factor for transcription factors, such as MYC, that drive aberrant cell proliferation when their expression is deregulated. CDK9 modulation offers an approach for attenuating dysregulation in such transcriptional programs.
Read the full summary ↓
As a result, numerous drug development campaigns to inhibit CDK9 kinase activity have been pursued. We validated that CDK9 inhibition triggers a compensatory mechanism that dampens its effect on MYC transcriptional programs and found that this resistance mechanism was absent when the Kinase is degraded. Importantly, CDK9 degradation is more effective than its inhibition for disrupting MYC transcriptional regulatory circuitry likely through the abrogation of both enzymatic and scaffolding functions of CDK9.
Published in
Targeted degradation of CDK9 potently disrupts the MYC-regulated network
Toure MA, Motoyama K, Xiang Y et al. · Cell chemical biology 2025 · PMID 40154489 · doi:10.1016/j.chembiol.2025.03.001
This dataset
Open GSE263153 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 GSE263153_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 PRJNA1095987 and SRA study SRP499635. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40154489) ↗
Study design
23 conditions, mostly with about 4 replicates each
MOLT4.veh.8, ×4 MOLT4.inh.8, ×4 MOLT4.deg.8, ×4 MOLT4.inh.4, ×4 MOLT4.deg.4, ×4 MOLT4.veh.2, ×4 MOLT4.inh.2, ×4 MOLT4.deg.2, ×4 +15 more

Supports a between-group comparison across 91 samples.

How we read this: 23 replicated groups read from 91 sample titles; they account for 91 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

+ 51 more — browse all 91 samples with per-sample file links →

Datasets on a similar topic

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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.