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Transcriptome analysis of oocytes and early embryos to demonstrate trancriptional regulation during mouse oocyte-to-embryo transition

GSE241388 Mus musculus (mouse) RNA-seq (gene expression) 32 samples Submitted 2025/01/20 Platform GPL21493
At a glance

RNA-seq (gene expression) · mouse · 32 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
32 samples: 16 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.
Paper
Deciphering transcription activity of mammalian early embryos unveils on/off of zygotic genome activation by protein translation/degradationCell reports · 2025
Summary (written by the submitters)
In this study, we performed RNA-seq to elucidate how transcriptional activities of mouse oocytes and preimplantation embryos are regulated to control oocyte-to-embryo transition. Through analyzing transcriptome alterations of transgenically-modified growing oocytes, early embryos from aged female, early embryos treated with drugs disturbing proteostasis, and embryonic stem cells treated with drugs disturbing proteostasis, we identified critical roles of proteostasis in transcriptional regulation of mouse oocytes and early embryos.
Published in
Deciphering transcription activity of mammalian early embryos unveils on/off of zygotic genome activation by protein translation/degradation
Zhang YR, Guo SM, Shi XY et al. · Cell reports 2025 · PMID 39823229 · doi:10.1016/j.celrep.2024.115215
This dataset
Open GSE241388 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 GSE241388_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 PRJNA1006851 and SRA study SRP456020. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39823229) ↗
Study design
16 conditions, mostly in duplicate
P14_Oo_K4M ×2 P14_Oo_WT ×2 AB22_CHX_Long ×2 AB22_MG132_Long ×2 AB22_WT_Long ×2 IVF12M2cell ×2 IVFAPH ×2 IVFCHX ×2 +8 more

Supports a between-group comparison across 32 samples.

How we read this: 16 replicated groups read from 32 sample titles; they account for 32 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

Search all mouse RNA-seq datasets in GEO →

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