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Single embryo total RNA sequencing to map the effect of maternal SETDB1 on the 2-celll and 8-cell transcriptome

GSE269417 Mus musculus (mouse) RNA-seq (gene expression) 37 samples Submitted 2025/12/28 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 37 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
37 samples: 15 × Setdb1 2c matKO single embryo vs 8 × Setdb1 8c matKO single embryo vs 8 × Setdb1 8c control single embryo vs 6 × Setdb1 2c control single embryoGroups 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
SETDB1 enables development beyond cleavage stages by extinguishing the MERVL-driven two-cell totipotency transcriptional program in the mouse embryoeLife · 2026
Summary (written by the submitters)
Embryos with maternal mutation of the H3K9 methyltransferase SETDB1 die before implantation. We tested the role of maternal SETDB1 in the timely processes of the preimplantation stage embryo. Using single embryo total RNA sequencing from 2-cell and 8-cell embryos, we found that maternal SETDB1 is required for switching off maternal transcripts by the 2-cell stage, minor ZGA transcripts by the 2-cell stage, and major ZGA transcripts by the 8-cell stage.
Read the full summary ↓
By timely extinguishing of endogenous retroviruses, oocyte-specific ERVL-MaLRs, many oocyte-specific genes, MERVLs, MERVL LTR-driven chimeric transcripts and ZGA genes as well as KRAB ZF genes, maternal SETDB1 secures the proper transition from totipotency to pluripotency.
Published in
SETDB1 enables development beyond cleavage stages by extinguishing the MERVL-driven two-cell totipotency transcriptional program in the mouse embryo
Zeng TB, Fu Z, Majewski MF et al. · eLife 2026 · PMID 41697236 · doi:10.7554/eLife.109248
This dataset
Open GSE269417 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 GSE269417_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 PRJNA1121885 and SRA study SRP512756. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41697236) ↗
Study design
15 × Setdb1 2c matKO single embryo vs 8 × Setdb1 8c matKO single embryo vs 8 × Setdb1 8c control single embryo vs 6 × Setdb1 2c control single embryo

Supports a between-group comparison across 37 samples.

How we read this: 4 replicated groups read from 37 sample titles; they account for 37 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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