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Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm.

GSE293151 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2025/07/21 Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 24 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
24 samples: 8 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.
Paper
Enhancer remodeling by OTX2 directs specification and patterning of mammalian definitive endodermDevelopmental cell · 2025
Summary (written by the submitters)
We discovered a role for the transcription factor OTX2 in formation of mouse definitive endoderm (DE). We used RNAseq to measure changes in gene expression and identify OTX2-regulated genes during directed differentiation of EpiSCs to Primitive Streak (PS) intermediates and DE
Published in
Enhancer remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm
Ee LS, Medina-Cano D, Goetzler E et al. · Developmental cell 2025 · PMID 40834858 · doi:10.1016/j.devcel.2025.07.020
This dataset
Open GSE293151 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 GSE293151_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 PRJNA1242889 and SRA study SRP573687. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40834858) ↗
Study design
8 conditions, mostly in triplicate
DE1_dTAG ×3 DE1_DMSO ×3 DE2_dTAG ×3 DE2_DMSO ×3 EPI_dTAG ×3 EPI_DMSO ×3 PS_dTAG ×3 PS_DMSO ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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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