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Mapping putative enhancers in mouse oocyte and early embryo reveals TCF3/12 as key folliculogenesis regulators

GSE217970 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 164 samples Submitted 2024/03/23 Platform GPL21273Platform GPL17021
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 164 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
164 samples: 140 distinct titles, 20 of them repeatedGroups 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
Mapping putative enhancers in mouse oocytes and early embryos reveals TCF3/12 as key folliculogenesis regulatorsNature cell biology · 2024
Summary (written by the submitters)
Dynamic epigenomic reprogramming occurs during mammalian oocyte maturation and early development. However, the underlying transcription circuitry remains poorly characterized. By mapping cis-regulatory elements using H3K27ac, we identified putative enhancers in mouse oocytes and early embryos distinct from those in adult tissues, enabling global transitions of regulatory landscapes around fertilization and implantation.
Read the full summary ↓
Gene deserts harbor prevalent putative enhancers in fully-grown oocytes linked to oocyte-specific gene and repeat activation. Embryo-specific enhancers are primed prior to zygotic genome activation and are restricted by oocyte-inherited H3K27me3. Putative enhancers in oocytes often manifest H3K4me3, bidirectional transcription, Pol II binding, and can drive transcription in STARR-seq and a reporter assay. Finally, motif analysis of these elements identified crucial regulators of oogenesis – TCF3 and TCF12, the deficiency of which impairs activation of key oocyte genes and folliculogenesis. These data reveal distinctive regulatory landscapes and their interacting TFs that underpin the development of mammalian oocytes and early embryos.
Published in
Mapping putative enhancers in mouse oocytes and early embryos reveals TCF3/12 as key folliculogenesis regulators
Liu B, He Y, Wu X et al. · Nature cell biology 2024 · PMID 38839978 · doi:10.1038/s41556-024-01422-x
This dataset
Open GSE217970 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 GSE217970_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 PRJNA901494 and SRA study SRP407926. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38839978) ↗
Study design
140 distinct titles, 20 of them repeated
p10_Dam ×4 p10_Lamin ×4 2cell_early_H3K27ac ×2 2cell_late_H3K27ac ×2 2cell_late_Parthenogenetic_Eed_control_H3K27ac ×2 2cell_late_Parthenogenetic_Eed_KO_H3K27ac ×2 8cell_H3K27ac ×2 FGO_H3K27ac ×2 +12 more

How we read this: Read from 164 sample titles: 140 distinct titles with little repetition. 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

+ 124 more — browse all 164 samples with per-sample file links →

Datasets on a similar topic

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