GEO DataSets

(Submitter supplied) Germ cell specification is accompanied by epigenetic remodeling, the scale and specificity of which are unclear. Here, we quantitatively delineate chromatin dynamics during induction of mouse embryonic stem cells (ESCs) to epiblast-like cells (EpiLCs) and from there into primordial germ cell-like cells (PGCLCs), revealing large-scale reorganization of chromatin signatures including H3K27me3 and H3K9me2 patterns. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15907

54 Samples

Download data: BED, TDF

(Submitter supplied) We re-analyzed gene expression in the primordial germ cell (PGC) specification pathway in vitro, by using previously deposited microarray data. The germ cell lineage produces either spermatozoa or oocytes and, by their fusion, creates zygotes with full developmental potential, thereby perpetuating and diversifying organisms' genetic as well as epigenetic information across generations. In mice, PGCs are specified in the most posterior part of epiblast (monolayer epitherium-like cells, from which the whole embryonic part of conceptus will be derived) around embryonic day (E) 6.25 by a cytokine BMP4. more...

Organism:

Mus musculus

Type:

Expression profiling by array; Third-party reanalysis

Platform:

GPL1261

6 Samples

Download data: CEL, TXT

(Submitter supplied) Nanog, a core pluripotency factor in the inner cell mass of blastocysts, is also expressed in unipotent primordial germ cells (PGC) in mice1, where its precise role is yet unclear2-4. We investigated this in an in vitro model, where naïve pluripotent embryonic stem cells (ESCs) cultured in bFGF/ActivinA develop as epiblast-like cells (EpiLCs), and gain competence for PGC-like fate5. Consequently, bone morphogenetic protein (BMP4), or ectopic expression of key germline transcription factors Prdm1/ Prdm14/ Tfap2c, directly induce PGC-like cells (PGCLCs) in EpiLCs, but not in ESCs6-8. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL6887 GPL13112

18 Samples

Download data: BEDGRAPH

(Submitter supplied) Nanog, a core pluripotency factor in the inner cell mass of blastocysts, is also expressed in unipotent primordial germ cells (PGCs) in mice, where its precise role is yet unclear. We investigated this in an in vitro model, in which naive pluripotent embryonic stem (ES) cells cultured in basic fibroblast growth factor (bFGF) and activin A develop as epiblast-like cells (EpiLCs) and gain competence for a PGC-like fate. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: BEDGRAPH

(Submitter supplied) Nanog, a core pluripotency factor in the inner cell mass of blastocysts, is also expressed in unipotent primordial germ cells (PGC) in mice1, where its precise role is yet unclear2-4. We investigated this in an in vitro model, where naïve pluripotent embryonic stem cells (ESCs) cultured in bFGF/ActivinA develop as epiblast-like cells (EpiLCs), and gain competence for PGC-like fate5. Consequently, bone morphogenetic protein (BMP4), or ectopic expression of key germline transcription factors Prdm1/ Prdm14/ Tfap2c, directly induce PGC-like cells (PGCLCs) in EpiLCs, but not in ESCs6-8. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

6 Samples

Download data: TXT

(Submitter supplied) Germ cells ensure reproduction and heredity in metazoans. Primordial germ cells (PGCs) in mice are induced in pluripotent epiblasts by BMP4 and WNT3, yet their mechanism of action remains unclear. Here, using in vitro PGC specification system, we show that WNT3 induces many transcription factors associated with mesoderm in epiblast-like cells (EpiLCs) through b-CATENIN. Among these, T (BRACHYURY), a classical and conserved mesodermal factor, was essential for robust activation of Blimp1 and Prdm14, two of the germline determinants. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15907

9 Samples

Download data: BED, TDF, WIG

(Submitter supplied) The germ cell lineage ensures reproduction and heredity in metazoans. Primordial germ cells (PGCs) in mice are induced in pluripotent epiblast cells by BMP4 and WNT3, yet their mechanism of action remains elusive. Here, using in vitro PGC specification system, we show that WNT3, but not BMP4, induces many transcription factors associated with mesoderm in epiblast-like cells (EpiLCs) through beta-CATENIN. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS4870

Platform:

GPL1261

23 Samples

Download data: CEL

Analysis of Wnt3+/+ and Wnt3-/- embryonic stem cell-induced, pluripotent epiblast-like cells stimulated with cytokines (BMP4, Wnt3a, or BMP4+Wnt3a) for up to 36 hrs to induce primordial germ cells (PGCs). Results provide insight into molecular mechanisms by which BMP4/WNT3 signaling specifies PGCs.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 genotype/variation, 4 protocol, 4 time sets

Platform:

GPL1261

Series:

GSE49689

23 Samples

Download data: CEL

(Submitter supplied) A small subgroup of embryonic stem cells (ESCs) exhibit molecular features similar to those of 2-cell (2C) embryos. These so-called 2C-like cells display highly relaxed chromatin architecture and expanded developmental potential. However, it remains elusive whether 2C-like cells and 2-cell embryos share similar epigenetic features. Here, we map the genome-wide profiles of histone H3K4me3 and H3K27me3 in 2C-like cells. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

24 Samples

Download data: BW

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

Organism:

Mus musculus

Type:

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

Platform:

GPL17021

74 Samples

Download data: TSV

(Submitter supplied) To follow the changes in the transcriptional programs accompanying the specification, maintenance and differentiation of the adult ISCs we sequenced whole transcriptomes of embryonic intestinal epithelium progenitors (at E12.5 and E14.5), adult ISCs and their differentiated progenies, the majority of which are absorptive enterocytes. EpCAM positive embryonic gut epithelium was isolated from dissected small intestines using fluorescence activated cell sorting (FACS). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: TSV

(Submitter supplied) We assessed whether changes in DNA methylation were associated with the regulation of ISC signature genes. Methylated regions of DNA from whole genome were isolated using Methyl Binding Domain pull-down followed by sequencing (MBD-seq). The size of DNA fragments was between 120 to 170 bp, which provides a resolution at nucleosome level.

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17021

8 Samples

Download data: TSV

(Submitter supplied) To determine chromatin changes associated with ISCs specification we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) using 2x105 FACS purified E12.5 or E14.5 embryonic intestinal epithelial cells, Lgr5+ adult ISCs and enterocytes.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: TSV

(Submitter supplied) To determine chromatin changes associated with ISCs specification we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) using 2x105 FACS purified E12.5 or E14.5 embryonic intestinal epithelial cells, Lgr5+ adult ISCs and enterocytes.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

16 Samples

Download data: TSV

(Submitter supplied) To determine chromatin changes associated with ISCs specification we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) using 2x10e5 FACS purified E12.5 or E14.5 embryonic intestinal epithelial cells, Lgr5+ adult ISCs and enterocytes.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: TSV

(Submitter supplied) To determine chromatin changes associated with ISCs specification we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) using 2x10e5 FACS purified E12.5 or E14.5 embryonic intestinal epithelial cells, Lgr5+ adult ISCs and enterocytes.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

14 Samples

Download data: TSV

(Submitter supplied) Pluripotent stem cells provide a powerful system to dissect the underlying molecular dynamics that regulate cell fate changes during mammalian development. Here we report the integrative analysis of genome wide binding data for 38 transcription factors with extensive epigenome and transcriptional data across the differentiation of human embryonic stem cells to the three germ layers. We describe core regulatory dynamics and show the lineage specific behavior of selected factors. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

204 Samples

Download data: BIGBED, BW, TXT

(Submitter supplied) [This SuperSeries is composed of the SubSeries listed below.] Embryogenesis requires the precise activation and repression of many transcriptional regulators. The Polycomb group proteins and the associated H3K27me3 histone mark are essential to maintain the inactive state of many of these genes. Mammalian Hox genes are targets of Polycomb proteins and form local 3D clusters centered on the H3K27me3 mark. more...

Organism:

Mus musculus

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

36 Samples

Download data: BEDGRAPH, BW

(Submitter supplied) Embryogenesis requires the precise activation and repression of many transcriptional regulators. The Polycomb group proteins and the associated H3K27me3 histone mark are essential to maintain the inactive state of many of these genes. Mammalian Hox genes are targets of Polycomb proteins and form local 3D clusters centered on the H3K27me3 mark. More distal contacts have also been described, yet their selectivity, dynamics and relation to other layers of chromatin organization remained elusive. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

32 Samples

Download data: BEDGRAPH, BW

(Submitter supplied) Embryogenesis requires the precise activation and repression of many transcriptional regulators. The Polycomb group proteins and the associated H3K27me3 histone mark are essential to maintain the inactive state of many of these genes. Mammalian Hox genes are targets of Polycomb proteins and form local 3D clusters centered on the H3K27me3 mark. More distal contacts have also been described, yet their selectivity, dynamics and relation to other layers of chromatin organization remained elusive. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: BW