GEO series
A CDK11-dependent RNA polymerase II pause-release checkpoint precedes CDK9-mediated transition to transcriptional elongation [ChIP-Seq]
GSE280208
Homo sapiens (human)
ChIP-seq / ATAC-seq (genome binding and open chromatin)
33 samples
Submitted 2025/08/25
Platform GPL18573
At a glance
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 33 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)
- Samples
- 33 samples: 30 distinct titles, 3 of them repeatedGroups 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
- A CDK11-dependent RNA polymerase II pause-checkpoint precedes CDK9-mediated transition to transcriptional elongationMolecular cell · 2025
Summary (written by the submitters)
Controlled gene expression is achieved through the intricate regulation of RNA polymerase II (Pol II) progression through transcription-cycle checkpoints. The pausing checkpoint, where Pol II temporarily stalls prior to release into transcriptional elongation, is a key molecular mechanism that fine-tunes gene expression. While the critical contribution of cyclin-dependent-kinase 9 (CDK9) for Pol II pause-release is well established, the requirement for other CDKs has not been fully elucidated.
Read the full summary ↓
Here we identify a new role for CDK11 in the Pol II pausing-to-elongation transition at a checkpoint that is distinct and independent from CDK9. Selective CDK11 inhibition results in genome-wide stalling of Pol II at transcription-start-site (TSS) proximal regions and acute RNA synthesis ablation near the beginning of transcriptional units. High-resolution chromatin-immunoprecipitation and precision-nuclear-run-on assays reveals spatial differences between CDK11- and CDK9-dependent Pol II pause sites, with CDK11 regulating Pol II closer to the TSS. Cancer cells exhibit profound reliance on functional CDK11, with selective CDK11 inhibition providing therapeutic efficacy in pre-clinical in vivo models of leukaemia and lymphoma, demonstrating the importance of CDK11-dependent Pol II regulation for aggressive haematological malignancies.
Published in
Devlin JR, Martin B, Bartonicek N et al.
· Molecular cell 2025
· PMID 40858114
· doi:10.1016/j.molcel.2025.08.001
This dataset
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.
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 GSE280208_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1177353 and SRA study SRP540589. Searching any of these in the dataset finder brings you back here.
Study design
30 distinct titles, 3 of them repeated
ChIP-nexus, Pol II CTD4H8, THP1, DMSO 2 hours… ×2
ChIP-nexus, Pol II CTD4H8, THP1, OTS964 156nM… ×2
ChIP-nexus, Pol II CTD4H8, THP1, AZ5576 170nM… ×2
How we read this: Read from 33 sample titles: 30 distinct titles with little repetition. 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
- GSM8592201 ChIP-seq, Pol II CTD4H8, THP1, DMSO 2 hours
- GSM8592202 ChIP-seq, Pol II CTD4H8, THP1, OTS964 156nM 2 hours
- GSM8592203 ChIP-seq, Pol II CTD4H8, THP1, AZ5576 170nM 2 hours
- GSM8592204 ChIP-seq, Pol II CTD4H8, THP1 FLAG-CDK11-AID, Ethanol 4 hours
- GSM8592205 ChIP-seq, Pol II CTD4H8, THP1 FLAG-CDK11-AID, Auxin 0.5mM 4 hours
- GSM8592206 ChIP-seq, Pol II CTD4H8, THP1 FLAG-CDK11-AID no OsTIR control, Ethanol 4 hours
- GSM8592207 ChIP-seq, Pol II CTD4H8, THP1 FLAG-CDK11-AID no OsTIR control, Auxin 0.5mM 4 hours
- GSM8592208 ChIP-seq, Pol II CTD4H8, THP1 untreated
- GSM8592209 ChIP-seq, CDK11, THP1 untreated
- GSM8592210 ChIP-seq, input, THP1 untreated
- GSM8592211 ChIP-seq, CDK11, THP1, DMSO 2 hours
- GSM8592212 ChIP-seq, CDK11, THP1, OTS964 156nM 2 hours
- GSM8592213 ChIP-seq, CDK11, THP1, AZ5576 170nM 2 hours
- GSM8592214 ChIP-seq, CDK11, THP1 FLAG-CDK11-AID, Ethanol 4 hours
- GSM8592215 ChIP-seq, CDK11, THP1 FLAG-CDK11-AID, Auxin 0.5mM 4 hours
- GSM8592216 ChIP-seq, Pol II CTD4H8, THP1, DMSO only 2 hours,
- GSM8592217 ChIP-seq, Pol II CTD4H8,THP1, OTS964 2 hours
- GSM8592218 ChIP-seq, Pol II CTD4H8, THP1, LPS 3 hours
- GSM8592219 ChIP-seq, Pol II CTD4H8, THP1, LPS 3 hours and OTS964 2 hours
- GSM8592220 ChIP-seq, CDK11, THP1, DMSO only 2 hours,
- GSM8592221 ChIP-seq, CDK11,THP1, OTS964 2 hours
- GSM8592222 ChIP-seq, CDK11, THP1, LPS 3 hours
- GSM8592223 ChIP-seq, CDK11, THP1, LPS 3 hours and OTS964 2 hours
- GSM8592224 ChIP-nexus, Pol II CTD4H8, THP1, DMSO 2 hours, exp1
- GSM8592225 ChIP-nexus, Pol II CTD4H8, THP1, OTS964 156nM 2 hours, exp1
- GSM8592226 ChIP-nexus, Pol II CTD4H8, THP1, AZ5576 170nM 2 hours, exp1
- GSM8592227 ChIP-nexus, Pol II CTD4H8, THP1, DMSO 2 hours, exp2, rep1
- GSM8592228 ChIP-nexus, Pol II CTD4H8, THP1, DMSO 2 hours, exp2, rep2
- GSM8592229 ChIP-nexus, Pol II CTD4H8, THP1, OTS964 156nM 2 hours, exp2 rep1
- GSM8592230 ChIP-nexus, Pol II CTD4H8, THP1, OTS964 156nM 2 hours, exp2 rep2
- GSM8592231 ChIP-nexus, Pol II CTD4H8, THP1, AZ5576 170nM 2 hours, exp2, rep1
- GSM8592232 ChIP-nexus, Pol II CTD4H8, THP1, AZ5576 170nM 2 hours, exp2, rep2
- GSM8592233 ChIP-nexus, mouse IgG, THP1, untreated, exp2
Datasets on a similar topic
- GSE280102 A CDK11-dependent RNA polymerase II pause-release checkpoint precedes CDK9-mediated transition to transcriptional elongation [RNA-seq] 29 samples shares cdk11-dependent, pause-release, cdk9-mediated, polymerase, checkpoint, transition, elongation, precedes
- GSE292907 Selective CDK7 Inhibition Sensitizes Tumors to Topoisomerase I Inhibitor-Antibody Drug Conjugates by Blocking The Transition of The RNA polymerase II Initiation Complex into Elongation [ChIP-seq] 97 samples shares polymerase, transition, elongation
- GSE292860 Selective CDK7 Inhibition Sensitizes Tumors to Topoisomerase I Inhibitor-Antibody Drug Conjugates by Blocking The Transition of The RNA polymerase II Initiation Complex into Elongation [RNA-seq] 16 samples shares polymerase, transition, elongation
- GSE220318 Splicing Factor RBM22 Broadly Affects RNA Polymerase II 5' Pausing, Elongation Rate and Termination and Prevents Genome Instability 70 samples shares polymerase, elongation
- GSE235181 Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition 44 samples shares polymerase, transition
- GSE265881 Tripartite phosphorylation of SPT5 by CDK9 times pause release and tunes elongation rate of RNA polymerase II (ChIP-Seq) 72 samples shares polymerase, elongation
- GSE265883 Tripartite phosphorylation of SPT5 by CDK9 times pause release and tunes elongation rate of RNA polymerase II (CUT&RUN) 68 samples shares polymerase, elongation
- GSE220316 Splicing Factor RBM22 Broadly Affects RNA Polymerase II 5' Pausing, Elongation Rate and Termination and Prevents Genome Instability [ChIP-seq] 64 samples shares polymerase, elongation
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