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Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in mouse early embryos [RNA-seq]

GSE264615 Mus musculus (mouse) RNA-seq (gene expression) 123 samples Submitted 2024/10/14 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 123 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
123 samples: 20 conditions, mostly with about 8 replicates eachGroups 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
Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in early mouse embryoseLife · 2025
Summary (written by the submitters)
During the first lineage segregation, mammalian embryos generate the inner cell mass (ICM) and trophectoderm (TE). ICM gives rise to the epiblast (EPI) that forms all cell types of the body, an ability referred to as pluripotency. The molecular mechanisms that induce pluripotency in embryos remain incompletely elucidated. Using knockout (KO) mouse models in conjunction with low-input ATAC-seq and RNA-seq, we found that Oct4 and Sox2 gradually come into play in the early ICM, coinciding with the initiation of Sox2 expression.
Read the full summary ↓
Oct4 and Sox2 directly activate the pluripotency-related genes through the corresponding OCT-SOX enhancers in the early ICM. Furthermore, we observed a substantial reorganization of chromatin landscape and transcriptome from the morula to the early ICM stages, which was partially driven by Oct4 and Sox2, highlighting their pivotal role in promoting the developmental trajectory towards the ICM. Our study provides new insights into the establishment of the pluripotency network in mouse preimplantation embryos.
Published in
Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in early mouse embryos
Hou Y, Nie Z, Jiang Q et al. · eLife 2025 · PMID 40014376 · doi:10.7554/eLife.100735
This dataset
Open GSE264615 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 GSE264615_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 PRJNA1103262 and SRA study SRP503436. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40014376) ↗
Study design
20 conditions, mostly with about 8 replicates each
RNA-seq_Oct4_Ctrl_Morula ×8 RNA-seq_Oct4_KO_Morula ×8 RNA-seq_Oct4_Ctrl_EarlyICM ×8 RNA-seq_Oct4_KO_EarlyICM ×8 RNA-seqOct4_Ctrl_MWT_LateICM ×8 RNA-seq_Sox2_Ctrl_Morula ×8 RNA-seq_Sox2_KO_Morula ×8 RNA-seq_Sox2_Ctrl_EarlyICM ×8 +12 more

Supports a between-group comparison across 123 samples.

How we read this: 20 replicated groups read from 123 sample titles; they account for 123 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

+ 83 more — browse all 123 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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