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Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [CUTnTAG]

GSE294521 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 34 samples Submitted 2025/07/21 Platform GPL34290
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 34 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Mus musculus (mouse)
Samples
34 samples: 12 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 CUT&TAG to map H3K27ac- and H3K4me1-bound genomic regions and identify OTX2-bound enhancers 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 GSE294521 in finder → Find more mouse ChIP / ATAC / CUT&Tag 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 GSE294521_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1250439 and SRA study SRP578572. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40834858) ↗
Study design
12 conditions, mostly in triplicate
OTX2-dTAG_DE1_K4me1_DMSO ×3 OTX2-dTAG_DE1_K4me1_dTAG ×3 OTX2-dTAG_EPI_K4me1_DMSO ×3 OTX2-dTAG_EPI_K4me1_dTAG ×3 OTX2-dTAG_PS_K4me1_DMSO ×3 OTX2-dTAG_PS_K4me1_dTAG ×3 OTX2-dTAG_EPI_K27ac_DMSO ×3 OTX2-dTAG_EPI_K27ac_dTAG ×3 +4 more

Supports a between-group comparison across 34 samples.

How we read this: 12 replicated groups read from 34 sample titles; they account for 34 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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