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CTDP1 governs a unique RNAPII phospho-form and coordinates Mediator recruitment, transcription efficiency, and splicing

GSE312502 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 44 samples Submitted 2025/12/08 Platform GPL30215Platform GPL28330Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 44 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
Mus musculus (mouse)
Samples
44 samples: 22 conditions, mostly in duplicateGroups 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.
Summary (written by the submitters)
We previously reported that the RNA polymerase II (Pol II) subunit RPB7 interacts with the phosphatase CTDP1 to regulate transcription termination-reinitiation. Here, we demonstrate that CTDP1 specifically dephosphorylates a unique phospho-isoform of Pol II, which is modified at tyrosine 1, serine 5, and serine 7 (Tyr1, Ser5, Ser7) of its C-terminal domain.
Read the full summary ↓
Functionally, this regulation is critical for the recruitment of the Mediator complex to chromatin and for modulating Pol II transcriptional efficiency. Furthermore, by integrating phosphoproteomic and immunoprecipitation-mass spectrometry data, we show that CTDP1 also regulates the phosphorylation of numerous RNA splicing factors. Consequently, depletion of CTDP1 disrupts gene expression oscillations, leading to increased intron retention and aberrant splicing of cassette exons. These findings suggest that CTDP1 serves as a key integrator of transcription and splicing, potentially contributing to the regulation of circadian rhythms and the cell cycle.
This dataset
Open GSE312502 in finder → Find more mouse ChIP / ATAC / CUT&Tag 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 GSE312502_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1371117. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
22 conditions, mostly in duplicate
ChIP-Seq_mES_RPB1NTD_CTDP1-13h_dTAG-0min ×2 ChIP-Seq_mES_RPB1NTD_deadCTDP1-13h_dATG-0min ×2 ChIP-Seq_mES_RPB1NTD_deadCTDP1-13h_dATG-20min ×2 ChIP-Seq_mES_RPB1NTD_deadCTDP1-13h_dATG-40min ×2 ChIP-Seq_mES_RPB1NTD_deadCTDP1-13h_dATG-60min ×2 ChIP-Seq_mES_MED1_CTDP1-12h ×2 ChIP-Seq_mES_MED1_deadCTDP1-12h ×2 ChIP-Seq_mES_MED4_CTDP1-12h ×2 +14 more

Supports a between-group comparison across 44 samples.

How we read this: 22 replicated groups read from 44 sample titles; they account for 44 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

+ 4 more — browse all 44 samples with per-sample file links →

Datasets on a similar topic

Search all mouse ChIP / ATAC / CUT&Tag datasets in GEO →

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