GEO series

Functional dissection of enhancers in 2-Cell embryo with an in vitro model [ChIP-seq]

GSE283347 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 18 samples Submitted 2026/07/27 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 18 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: 18 samples: 8 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.

Summary (written by the submitters)

Zygotic genome activation (ZGA) marks the initial transcription event in embryogenesis, yet the mechanisms cis-regulating gene activation remain unclear due to material constraints. Here, we functionally dissect the enhancers across the mouse genome in DUX-induced 2C-like cells. Integrated analysis with the epigenetic modifications and RNA transcriptiome in both 2C-like cells and 2C embryos, regions which show enhancer activities and their potential downstream target gens were depicted.

Read the full summary ↓

Among them, a notable proportion of promoters exhibits enhancer activities in totipotent cells. Those promoter regions are characterized by elevated levels of open chromatin-associated epigenetic modifications, which correlate with enhanced gene expression during ZGA. Our data further reveal that class Ⅲ mouse endogenous retrovirus (MERV)-related enhancers are enriched in 2C-like cells and nearly half of MERVL-LTR (Mt2_mm) elements exhibit enhancer activities, which have been mapped and characterized within the genome. Intriguingly, enhancers identified in 2C-like cells augment the transcription in vivo when injected into the embryos. Furthermore, the deletion of enhancer regions in both 2C-like cells and embryos demonstrated their role in promoting the transcription of their adjacent downstream target genes, with one of the deletions impaired the early embryo development. This study enhances our understanding of the regulatory elements guiding ZGA.

This dataset

Open GSE283347 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 GSE283347_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 PRJNA1193495 and SRA study SRP548983. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

8 conditions, mostly in duplicate

GFP negative input ×2 GFP negative H3K4me1 ×2 GFP positive input ×2 GFP positive H3K4me1 ×2 GFP positive H3K4me3 ×2 GFP positive H3K27ac ×2 GFP negative H3K4me3 ×2 GFP negative H3K27ac ×2 +2 more

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 18 sample titles; they account for 16 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

GSM8660596 GFP negative input rep1 GFP negative input
GSM8660597 GFP negative H3K4me1 rep1 GFP negative H3K4me1
GSM8660598 GFP positive input rep1 GFP positive input
GSM8660599 GFP positive H3K4me1 rep1 GFP positive H3K4me1
GSM8660600 GFP negative input rep2 GFP negative input
GSM8660601 GFP positive input rep2 GFP positive input
GSM8660602 GFP negative H3K4me1 rep2 GFP negative H3K4me1
GSM8660603 GFP positive H3K4me1 rep2 GFP positive H3K4me1
GSM8660604 GFP positive H3K4me3 rep1 GFP positive H3K4me3
GSM8660605 GFP positive H3K27ac rep1 GFP positive H3K27ac
GSM8660606 GFP negative H3K4me3 rep1 GFP negative H3K4me3
GSM8660607 GFP negative H3K4me3 rep2 GFP negative H3K4me3
GSM8660608 GFP negative H3K27ac rep1 GFP negative H3K27ac
GSM8660609 GFP negative H3K27ac rep2 GFP negative H3K27ac
GSM8660610 GFP positive H3K4me3 rep2 GFP positive H3K4me3
GSM8660611 GFP positive H3K27ac rep2 GFP positive H3K27ac
GSM9797980 GFP negative p300
GSM9797981 GFP positive p300

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GSE283389 Functional dissection of enhancers in 2-Cell embryo with an in vitro model. 37 samples shares 2-cell, dissection, enhancers, embryo, vitro
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GSE247083 Lysosomal catabolic activity governs the exit of the murine totipotent 2-cell state by silencing early-embryonic retrotransposons 38 samples shares 2-cell, embryo
GSE278338 ChIP-seq to measure binding of NIPBL/MAU2, RAD21, and CTCF in mouse embryonic stem cells and neural progenitor cells 50 samples shares chip-seq, embryo
GSE339012 Mega-Enhancers Compartmentalize Transcriptionally Active Long Genes in the Brain [ChIP-Seq] 22 samples shares enhancers, chip-seq
GSE269433 Histone Deacetylase 1 (HDAC1) maintains the transcriptome of embryonic stem cells through regulating acetylation at crucial genomic sites [ChIP-seq] 18 samples shares chip-seq, embryo
GSE257545 Top2a Differentially Modulates Promoter Activity in Embryonic Stem Cells via Trim28 Recruitment and PRC2 Displacement [ChIP-Seq] 16 samples shares chip-seq, embryo

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