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Co-transcriptional RNA processing boosts zygotic genes and restrains noncoding transcription

GSE272962 Mus musculus (mouse) RNA-seq (gene expression) 25 samples Submitted 2026/06/06 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 25 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
25 samples: 10 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.
Summary (written by the submitters)
Transcription decodes protein-coding genes and interprets regulatory information embedded in the genome by generating RNA. In eukaryotes, gene transcription is coupled with RNA processing via the carboxyl terminal domain (CTD) of RNA polymerase (Pol) II to enhance mRNA production. Here we propose that co-transcriptional RNA processing is essential for zygotic gene activation (ZGA), which shifts from noncoding to protein-centered gene expression post-fertilization.
Read the full summary ↓
Truncating the Pol II CTD in mouse embryonic stem cells disrupts this coupling, halting global mRNA synthesis and causing widespread intergenic transcription. This triggers transcriptional and epigenetic reprogramming and nuclear reorganization towards totipotency, resembling early two-cell embryos before ZGA. Mechanistically, the CTD suppresses noncoding transcription by restraining polymerase activity on chromatin, but facilitates promoter-proximal pausing, transcription directionality, velocity, and elongation efficacy at genes through coupled RNA processing. The evolution of longer CTD lengths enhances gene activity, likely accommodating the increasingly abundant noncoding genome sequences in mammals.
This dataset
Open GSE272962 in finder → Find more mouse 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 GSE272962_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 PRJNA1139718 and SRA study SRP521928. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
10 conditions, mostly in triplicate
RPB1_CTD_AID_ESCs_EU_washoff_3h ×3 RPB1_CTD_AID_ESCs_EU_washoff_6h ×3 RPB1_CTD_AID_ESCs_EU_washoff_12h ×3 RPB1_CTD_AID_ESCs_EU_washoff_24h ×3 RPB1_CTD_AID_ESCs_EU_washoff_36h ×3 RPB1_CTD_AID_ESCs_EU_IAA_0h ×2 RPB1_CTD_AID_ESCs_EU_IAA_3h ×2 RPB1_CTD_AID_ESCs_EU_IAA_6h ×2 +2 more

Supports a between-group comparison across 25 samples.

How we read this: 10 replicated groups read from 25 sample titles; they account for 25 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
Datasets on a similar topic

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