GEO DataSets

(Submitter supplied) Chicken primordial germ cells (PGCs) have an epigenetic signature which differs from the one that mammalian PGCs acquire with their epigenome reprogramming during early embryonic development. In particular, chicken PGCs display a high global amount of histone H3 lysine 9 trimethylation (H3K9me3) compared to somatic cell types. We performed the genome-wide profiling of H3K9me3 and the transcriptome analysis on chicken PGCs compared to embryonic stem cells (ESCs) as a closely related, non germinal cell type.

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19005

3 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL19787 GPL19005

7 Samples

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(Submitter supplied) Chicken primordial germ cells (PGCs) have an epigenetic signature which differs from the one that mammalian PGCs acquire with their epigenome reprogramming during early embryonic development. In particular, chicken PGCs display a high global amount of histone H3 lysine 9 trimethylation (H3K9me3) compared to somatic cell types. We performed the genome-wide profiling of H3K9me3 and the transcriptome analysis on chicken PGCs compared to embryonic stem cells (ESCs) as a closely related, non germinal cell type.

Organism:

Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19787

4 Samples

Download data: CSV

(Submitter supplied) Prdm14 is a critical gene for specifying mouse primordial germ cells (PGCs). The changes in expression in mouse PGCs caused by mutations of the Prdm14 gene were investigated at the single-cell level using microarray analysis.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

30 Samples

Download data: CEL

(Submitter supplied) We performed whole-genome bisulfite sequencing of Dppa3 knockout fully grown oocytes (FGOs).

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL18480

4 Samples

Download data: TXT

(Submitter supplied) We performed whole-genome bisulfite sequencing and RNA-seq analysis of Stella knockout primordial germ cells (PGCs).

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL24247

15 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by array

Platforms:

GPL6885 GPL6887

5 Samples

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(Submitter supplied) Mouse primordial germ cells (PGCs) erase global DNA methylation (5mC) as part of the comprehensive epigenetic reprogramming that occurs during PGC development. 5mC plays an important role in maintaining stable gene silencing and repression of transposable elements (TE) but it is not clear how the extensive loss of DNA methylation impacts on gene expression and TE repression in developing PGCs. Using a novel epigenetic disruption and recovery screen and genetic analyses, we identified a core set of germline-specific genes that are dependent exclusively on promoter DNA methylation for initiation and maintenance of developmental silencing. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

2 Samples

Download data: TXT

(Submitter supplied) Mouse primordial germ cells (PGCs) erase global DNA methylation (5mC) as part of the comprehensive epigenetic reprogramming that occurs during PGC development. 5mC plays an important role in maintaining stable gene silencing and repression of transposable elements (TE) but it is not clear how the extensive loss of DNA methylation impacts on gene expression and TE repression in developing PGCs. Using a novel epigenetic disruption and recovery screen and genetic analyses, we identified a core set of germline-specific genes that are dependent exclusively on promoter DNA methylation for initiation and maintenance of developmental silencing. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

3 Samples

Download data: TXT

(Submitter supplied) Medaka PGCs methylomes were sequenced using whole genome bisulfite sequencing (WGBS)

Organism:

Oryzias latipes

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL23039

15 Samples

Download data: BEDGRAPH

(Submitter supplied) Epigenetic reprogramming including demethylation of DNA occurs in mammalian primordial germ cells (PGCs) and in early embryos, and is important for the erasure of imprints and epimutations, and the return to pluripotency. The extent of this reprogramming and its molecular mechanisms are poorly understood. We previously showed that the cytidine deaminases Aid and Apobec1 can deaminate 5-methylcytosine in vitro and in E coli, and in the mouse are expressed in tissues in which demethylation occurs. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL9250 GPL9185

12 Samples

Download data: TXT

(Submitter supplied) Transcription of endogenous retroviruses (ERVs) is inhibited by de novo DNA methylation during gametogenesis, a process initiated after birth in oocytes and at ~E15.5 in prospermatogonia. Earlier in germline development however, the genome, including most retrotransposons, is progressively demethylated, with young ERVK and ERV1 elements retaining intermediate methylation levels. As DNA methylation reaches a low point in E13.5 primordial germ cells (PGCs) of both sexes, we determined whether retrotransposons are marked by H3K9me3 and H3K27me3 using a recently developed low input ChIP-seq method. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL13112

28 Samples

Download data: BW, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20301 GPL24676

72 Samples

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(Submitter supplied) Epigenetic resetting in the mammalian germ line entailsacute DNA demethylation, which lays the foundation for gametogenesis, totipotency,and embryonic development. We characterize the epigenome of hypomethylated human primordial germ cells (hPGCs) to reveal mechanisms preventing the widespread derepression of genesand transposable elements (TEs). Along with the loss of DNA methylation, we show that hPGCsexhibit a profound reduction of repressive histone modifications resulting in diminished heterochromatic signaturesat most genesand TEsand the acquisition of a neutral or paused epigenetic state without transcriptional activation.Efficient maintenance of a heterochromatic state is limited to a subset of genomic loci, such asevolutionarily young TEsand some developmental genes, which require H3K9me3 and H3K27me3, respectively, forefficient transcriptional repression. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

8 Samples

Download data: XLSX

(Submitter supplied) Epigenetic resetting in the mammalian germ line entailsacute DNA demethylation, which lays the foundation for gametogenesis, totipotency,and embryonic development. We characterize the epigenome of hypomethylated human primordial germ cells (hPGCs) to reveal mechanisms preventing the widespread derepression of genesand transposable elements (TEs). Along with the loss of DNA methylation, we show that hPGCsexhibit a profound reduction of repressive histone modifications resulting in diminished heterochromatic signaturesat most genesand TEsand the acquisition of a neutral or paused epigenetic state without transcriptional activation.Efficient maintenance of a heterochromatic state is limited to a subset of genomic loci, such asevolutionarily young TEsand some developmental genes, which require H3K9me3 and H3K27me3, respectively, forefficient transcriptional repression. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: XLSX

(Submitter supplied) Epigenetic resetting in the mammalian germ line entailsacute DNA demethylation, which lays the foundation for gametogenesis, totipotency,and embryonic development. We characterize the epigenome of hypomethylated human primordial germ cells (hPGCs) to reveal mechanisms preventing the widespread derepression of genesand transposable elements (TEs). Along with the loss of DNA methylation, we show that hPGCsexhibit a profound reduction of repressive histone modifications resulting in diminished heterochromatic signaturesat most genesand TEsand the acquisition of a neutral or paused epigenetic state without transcriptional activation.Efficient maintenance of a heterochromatic state is limited to a subset of genomic loci, such asevolutionarily young TEsand some developmental genes, which require H3K9me3 and H3K27me3, respectively, forefficient transcriptional repression. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

54 Samples

Download data: NARROWPEAK

(Submitter supplied) Epigenetic resetting in the mammalian germ line entailsacute DNA demethylation, which lays the foundation for gametogenesis, totipotency,and embryonic development. We characterize the epigenome of hypomethylated human primordial germ cells (hPGCs) to reveal mechanisms preventing the widespread derepression of genesand transposable elements (TEs). Along with the loss of DNA methylation, we show that hPGCsexhibit a profound reduction of repressive histone modifications resulting in diminished heterochromatic signaturesat most genesand TEsand the acquisition of a neutral or paused epigenetic state without transcriptional activation.Efficient maintenance of a heterochromatic state is limited to a subset of genomic loci, such asevolutionarily young TEsand some developmental genes, which require H3K9me3 and H3K27me3, respectively, forefficient transcriptional repression. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: NARROWPEAK

(Submitter supplied) DNA methylation and hydroxymethylation in the genomes of mouse E12.5 primordial germ cells (PGCs), primordial germ cell-like cells (PGCLCs) isolated from 6-day culture embryoid bodies, and the precursor pluripotent stem cells [embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs)] and epiblast-like cells (EpiLCs)

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL15907

43 Samples

Download data: WIG

(Submitter supplied) Transcriptomes of mouse E12.5 primordial germ cells (PGCs), primordial germ cell-like cells (PGCLCs) isolated from 6-day culture embryoid bodies, and the precursor pluripotent stem cells [embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs)] and epiblast-like cells (EpiLCs)

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

25 Samples

Download data: CEL, XLSX

(Submitter supplied) Purpose: To identify molecular pathways underlying epigenetic reprogramming in early germ cell precursors, we examined global gene expression of wild type primordial germ cells using mRNA sequencing. Methods: Given the limited number of PGCs collected from E9.5 to E13.5 (ranging from 300 to 5000), we used a low-input RNA sequencing method, Smart-Seq. RNA libraries were pooled and sequenced by Illumina Hiseq. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: TXT