GEO series

Allelic genome-wide maps of open chromatin state in zygotes and early embryo

GSE92605 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 69 samples Submitted 2017/07/19 Platform GPL17021

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 69 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: 69 samples
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)

Mammalian sperm and oocytes have different epigenetic landscapes and are organized in different fashion. Following fertilization, the initially distinct parental epigenomes become largely equalized with the exception of certain loci including imprinting control regions. How parental chromatin becomes equalized and how imprinted genes escape this wave of reprogramming is largely unknown.

Read the full summary ↓

Here we generated high-resolution maps of parental allele-specific DNase I hypersensitive sites (DHSs) in zygotes and morula embryos by using physically-isolated parental pronuclei, as well as parthenogenetic (PG) and androgenetic (AG) embryos. Allelic transcriptome analyses revealed a high correlation between allelic DHSs and allelic gene expression not only in known imprinted genes but also in dozens of genes not previously known to be imprinted. Interestingly, we found that many paternally- expressed genes harbor paternal allele-specific DHSs (Ps-DHSs) that are highly enriched for histone H3K27 tri-methylation (H3K27me3) but devoid of DNA methylation in maternal allele. Importantly, ectopic removal of the H3K27me3 turns Ps-DHSs into bi- allelic DHSs and induces maternal allele derepression in genes that include maternal DNA methylation-independent imprinted genes Gab1, Sfmbt2, Slc38a4, and Phf17 (also known as Jade1). Thus, our study not only reveals parental allele-specific chromatin accessibility of preimplantation embryos, but also identifies maternal H3K27me3 as a DNA methylation- independent mechanism for genomic imprinting.

This dataset

Open GSE92605 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 GSE92605_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 PRJNA358118 and SRA study SRP095376. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 28723896) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 69 more — browse all 69 samples with per-sample file links →

Datasets on a similar topic

GSE264193 H3K27 dimethylation dynamics reveal stepwise establishment of facultative heterochromatin in early mouse embryos [ChIP-seq] 57 samples shares chromatin, embryo, early
GSE241378 Alternative splicing of a chromatin modifier alters the transcriptional regulatory programs of embryonic stem cell maintenance and neuronal differentiation. 36 samples shares chromatin, embryo
GSE262791 LaminB1 DamID, RNA-seq and Genome-wide analysis of replication timing in RIF1 depleted preimplantation mouse embryos 468 samples shares genome-wide, embryo
GSE200323 Establishment of chromatin architecture interplays with embryo hypertranscription 158 samples shares chromatin, embryo
GSE274493 The remodeling of bivalent chromatin is essential for mouse peri-implantation embryogenesis [CUT&Tag] 46 samples shares chromatin, embryo
GSE278416 3D Chromatin organization of signal-induced specific enhancers safeguards early ESC differentiation by promoting cluster gene expression 40 samples shares chromatin, early
GSE273309 Chromatin remodeler CHD4 establishes chromatin states required for ovarian reserve formation, maintenance, and germ cell survival 30 samples shares chromatin, state
GSE283483 Novel environment exposure drives temporally defined and region-specific chromatin accessibility and gene expression programs in the hippocampus 160 samples shares chromatin

Search all mouse ChIP / ATAC / CUT&Tag datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.