The TFIIH kinase CDK7 governs RNA polymerase II initiation, elongation, termination, and RNA processing
RNA-seq (gene expression) · human · 30 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
- 30 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
- Multi-omics and biochemical reconstitution reveal CDK7-dependent mechanisms controlling RNA polymerase II function at gene 5'- and 3'-endsbioRxiv : the preprint server for biology · 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 GSE228346_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 PRJNA949515 and SRA study SRP429713. 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 30 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.
- GSM7119231 DMSO_0_R1 [PRO-seq]
- GSM7119232 DMSO_0_R2 [PRO-seq]
- GSM7119233 SY5609_0_R1 [PRO-seq]
- GSM7119234 SY5609_0_R2 [PRO-seq]
- GSM7119235 DMSO_20_R1 [PRO-seq]
- GSM7119236 DMSO_20_R2 [PRO-seq]
- GSM7119237 SY5609_20_R1 [PRO-seq]
- GSM7119238 SY5609_20_R2 [PRO-seq]
- GSM7119239 DMSO_45_R1 [PRO-seq]
- GSM7119240 DMSO_45_R2 [PRO-seq]
- GSM7119241 SY5609_45_R1 [PRO-seq]
- GSM7119242 SY5609_45_R2 [PRO-seq]
- GSM7119255 DMSO_0_R1 DMSO_0
- GSM7119256 DMSO_0_R2 DMSO_0
- GSM7119257 DMSO_0_R3 DMSO_0
- GSM7119258 SY5609_0_R1 SY5609_0
- GSM7119259 SY5609_0_R2 SY5609_0
- GSM7119260 SY5609_0_R3 SY5609_0
- GSM7119261 DMSO_30_R1 DMSO_30
- GSM7119262 DMSO_30_R2 DMSO_30
- GSM7119263 DMSO_30_R3 DMSO_30
- GSM7119264 SY5609_30_R1 SY5609_30
- GSM7119265 SY5609_30_R2 SY5609_30
- GSM7119266 SY5609_30_R3 SY5609_30
- GSM7119267 DMSO_120_R1 DMSO_120
- GSM7119268 DMSO_120_R2 DMSO_120
- GSM7119269 DMSO_120_R3 DMSO_120
- GSM7119270 SY5609_120_R1 SY5609_120
- GSM7119271 SY5609_120_R2 SY5609_120
- GSM7119272 SY5609_120_R3 SY5609_120
- 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 cdk7, polymerase, initiation, 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 cdk7, polymerase, initiation, elongation
- GSE218269 CDK7 kinase activity promotes RNA polymerase II promoter escape by facilitating initiation factor release 100 samples shares cdk7, polymerase, initiation
- GSE220318 Splicing Factor RBM22 Broadly Affects RNA Polymerase II 5' Pausing, Elongation Rate and Termination and Prevents Genome Instability 70 samples shares termination, 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 termination, polymerase, elongation
- 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
- GSE223058 TFIIIC and MYCN link the three-dimensional chromatin structure of promoters to transcription termination of stalled RNA polymerase 62 samples shares termination, polymerase
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.