GEO DataSets

(Submitter supplied) Germ cells are vital for transmitting genetic information from one generation to the next and for maintaining the continuation of species. Here, we analyze the transcriptome of human primordial germ cells (PGCs) from the migrating stage to the gonadal stage at single-cell and single-base resolutions. Human PGCs show unique transcription patterns involving the simultaneous expression of both pluripotency genes and germline-specific genes, with a subset of them displaying developmental stage-specific features. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL16791 GPL11154

364 Samples

Download data: BED, TXT

(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

Download data

(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) 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) 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) PGCs undergo two distinct stages of demethylation before reaching a hypomethylated ground state at E13.5. Stage 1 occurs between E7.25- E9.5 in which PGCs experience a global loss of cytosine methylation. However, discreet loci escape this global loss of methylation and between E10.5-E13.5, stage 2 of demethylation takes place. In this stage these loci are targeted by Tet1 and Tet2 leading to the loss of the remaining methylation and resulting in the epigenetic ground state. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

37 Samples

Download data: DIFF, TXT

(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) Epigenetic reprogramming, characterized by loss of cytosine methylation and histone modifications, occurs during mammalian development in primordial germ cells (PGCs). Here we provide a detailed map of cytosine methylation on a large portion of the genome in developing male and female PGCs isolated from mouse embryos.

Organism:

Mus musculus

Type:

Methylation profiling by genome tiling array

Platform:

GPL9485

8 Samples

Download data: PAIR

(Submitter supplied) During embryonic development, large-scale reprogramming occurs in primordial germ cells (PGCs) at the level of both DNA demethylation and histone modifications. While much is known about epigenetic changes, it still remains unclear how this chromatin state impacts the transcriptome and development of the germline. We have used cell-number normalised (CNN) RNA-seq to document the striking upregulation of the germ cell transcriptome at E13.5 compared to neighboring somatic cells of the embryonic gonad. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

12 Samples

Download data: TXT

(Submitter supplied) Generation of research quality, clinically relevant cell types in vitro from human pluripotent stem cells (hPSCs) requires detailed understanding of the equivalent cell types in humans. Here we analyzed 130 human fetal samples at 6-20 weeks of development and identified the stages in which human cKIT+ primordial germ cells (PGCs), the precursors of gametes, undergo whole genome epigenetic reprogramming and ultimately initiation of imprint erasure with loss of both 5mC and 5-hydroxy-mC at differentially methylated regions. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

7 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

26 Samples

Download data: TXT

(Submitter supplied) We performed WGBS analyses on 6 human fetal samples at 53-137 days of development, 4 female and 2 male. We show that methylation reprogramming in the human germline is global yet incomplete with exons, 3’UTRs and human-specific transposons remaining methylated.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

7 Samples

Download data: TXT

(Submitter supplied) We performed RNA-Seq analyses on 15 human fetal samples at 53-137 days of development, 9 female and 5 male, and identified the transcriptional changes during the transition of human cKIT+ primordial germ cells (PGCs), the precursors of gametes, to the generation of Advanced Germline Cells. Comparing the transcriptional profile of PGCs to that of H1 and UCLA1 hESCs identifies differences between the two cell types and pinpoints molecules that can be used in the development of in vitro germ cell differentiation protocols starting from human pluripotent stem cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

19 Samples

Download data: TXT

(Submitter supplied) Gametes are highly specialised cells that can give rise to the next generation through their ability to generate a totipotent zygote. In mouse, germ cells are first specified in the developing embryo as primordial germ cells (PGCs) starting around embryonic day (E) 6.25. Following subsequent migration into the developing gonad, PGCs undergo a wave of extensive epigenetic reprogramming at E10.5/E11.5, including genome-wide loss of 5-methylcytosine (5mC). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

14 Samples

Download data: TXT

(Submitter supplied) Gametes are highly specialised cells that can give rise to the next generation through their ability to generate a totipotent zygote. In mouse, germ cells are first specified in the developing embryo as primordial germ cells (PGCs) starting around embryonic day (E) 6.25. Following subsequent migration into the developing gonad, PGCs undergo a wave of extensive epigenetic reprogramming at E10.5/E11.5, including genome-wide loss of 5-methylcytosine (5mC). more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL13112 GPL17021

69 Samples

Download data: TXT

(Submitter supplied) Gametes are highly specialised cells that can give rise to the next generation through their ability to generate a totipotent zygote. In mouse, germ cells are first specified in the developing embryo as primordial germ cells (PGCs) starting around embryonic day (E) 6.25. Following subsequent migration into the developing gonad, PGCs undergo a wave of extensive epigenetic reprogramming at E10.5/E11.5, including genome-wide loss of 5-methylcytosine (5mC). more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13112

7 Samples

Download data: BED

(Submitter supplied) Gametes are highly specialised cells that can give rise to the next generation through their ability to generate a totipotent zygote. In mouse, germ cells are first specified in the developing embryo as primordial germ cells (PGCs) starting around embryonic day (E) 6.25. Following subsequent migration into the developing gonad, PGCs undergo a wave of extensive epigenetic reprogramming at E10.5/E11.5, including genome-wide loss of 5-methylcytosine (5mC). more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17021

18 Samples

Download data: TXT