GEO DataSets

(Submitter supplied) To capture the Zeb2-dependent transcriptional changes in early cell state/fate decisions we performed RNA-seq on Zeb2 control and Zeb2 knockout cells. We chose three stages, which correspond in control ESCs to the naive pluripotent state (d0; very low amounts of Zeb2 mRNA), multipotent progenitors (d4, low Zeb2 mRNA/protein) and early neural progenitors (d6, high Zeb2 mRNA/protein), respectively.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

18 Samples

Download data: TXT, XLSX

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL17021 GPL13112

30 Samples

Download data

(Submitter supplied) In this study we performed temporal profiling of DNA methylation by RRBseq of differentiating mouse embryonic stem cells using an embryoid body protocol. Analysis at d0, d4 and d6 revealed that Zeb2 deficient mESC lose their initially acquired DNA methylation at d6.

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: BEDGRAPH, XLSX

(Submitter supplied) Primordial germ cells (PGCs) are specified from epiblast cells in mice. Genes associated with naïve pluripotency are transiently repressed in the transition from inner cell mass (ICM) to epiblast cells, followed by their upregulation soon after PGC specification. However, the molecular mechanisms underlying the reactivation of pluripotency genes are poorly characterized. Here, we exploited in vitro differentiation of epiblast-like cells (EpiLCs) from embryonic stem cells (ESCs) to elucidate the molecular and epigenetic functions of PR domain-containing 14 (PRDM14). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11180

6 Samples

Download data: CEL

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

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17021 GPL21103

28 Samples

Download data

(Submitter supplied) Gastrulation in the early post-implantation stage mammalian embryo begins when epiblast cells ingress to form the primitive streak or develop as the embryonic ectoderm. The DNA dioxygenase Tet1 is highly expressed in the epiblast and yet continues to regulate lineage specification during gastrulation when its expression is diminished. Here, we show how Tet1 plays a pivotal role upstream of germ layer lineage bifurcation. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17021 GPL21103

16 Samples

Download data: BW

(Submitter supplied) Gastrulation in the early post-implantation stage mammalian embryo begins when epiblast cells ingress to form the primitive streak or develop as the embryonic ectoderm. The DNA dioxygenase Tet1 is highly expressed in the epiblast and yet continues to regulate lineage specification during gastrulation when its expression is diminished. Here, we show how Tet1 plays a pivotal role upstream of germ layer lineage bifurcation. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

12 Samples

Download data: BW

(Submitter supplied) Unlimited self-renewal and developmental pluripotency are hallmarks of embryonic stem cells. Both properties are precisely controlled by the extrinsic signals and intrinsic factors and have been extensively investigated. However, factors capable of converting ES cells to extra-embryonic lineages have been poorly studied. Here we found that overexpression of Ssbp3 dramatically up-regulated trophoblast specific markers. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

4 Samples

Download data: CEL

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

Organism:

Mus musculus

Type:

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

Platform:

GPL17021

16 Samples

Download data: BED, BEDGRAPH, TSV

(Submitter supplied) Pluripotent cell identity comprises a spectrum of cell states including naive and primed states, which are typified by mouse embryonic stem cells (ESCs) and epiblast-derived stem cells (EpiSCs), respectively. Here we define a pluripotent cell fate (PCF) gene signature based on RNA-seq analysis associated with naive and primed pluripotency acquisition, and identify Zfp281 as a key transcriptional regulator for primed pluripotency and also as a barrier to achieve the naive pluripotency of both mouse and human ESCs.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

14 Samples

Download data: TSV

(Submitter supplied) Pluripotent cell identity comprises a spectrum of cell states including naive and primed states, which are typified by mouse embryonic stem cells (ESCs) and epiblast-derived stem cells (EpiSCs), respectively. Here we define a pluripotent cell fate (PCF) gene signature based on RNA-seq analysis associated with naive and primed pluripotency acquisition, and identify Zfp281 as a key transcriptional regulator for primed pluripotency and also as a barrier to achieve the naive pluripotency of both mouse and human ESCs.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

2 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) The goal of this study is to analyse the transcriptome of WT and Myc-overexpressing ESCs in iMOS T1-Myc mosaic cultures.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

9 Samples

Download data: TXT

(Submitter supplied) The goal is to examine the transcriptome of ESCs with different Myc levels

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

9 Samples

Download data: TXT

(Submitter supplied) Zinc finger E-box-binding homeobox 2 (ZEB2, also known as SMAD interacting protein 1 or Zfhx1b) protein is a transcription factor involved in the transforming growth factor β (TGFβ) and bone morphogenetic proteins (BMPs) signaling pathways. ZEB2 is a two-handed zinc-finger closely related to ZEB1 (ZFHX1a/δEF1) and it is present in many tissues including cardiac and skeletal muscles. Skeletal muscle development and adult myogenesis are regulated by helix-loop-helix proteins, including MyoD, Myf5, myogenin and MRF-4. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

23 Samples

Download data: TXT

(Submitter supplied) Genomic imprinting, resulting in parent-of-origin specific gene expression, plays a critical role in mammalian development. Here, we perform allele-specific RNA-Seq on isogenic B6D2F1 mice to assay imprinted genes in tissues from early embryonic stages and in pluripotent cell lines. For the cell lines, we include embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs) derived from fertilized embryos or from embryos obtained after nuclear transfer (NT), as well as B6D2F1 ESCs and EpiSCs derived after parthenogenetic activation (PGA). more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL11002 GPL19057 GPL13112

22 Samples

Download data: WIG

(Submitter supplied) During early mammalian development transient pools of pluripotent cells emerge that can be immortalised upon stem cell derivation. The pluripotent state, "naïve" or "primed", depends on the embryonic stage and derivation conditions used. Here we analyse the temporal gene expression patterns of mouse, cattle and porcine embryos at stages that harbour different types of pluripotent cells. We document conserved and divergent traits in gene expression, and identify predictor genes shared across the species that are associated with pluripotent states in vivo and in vitro Amongst these are the pluripotency-linked genes Klf4 and Lin28b The novel genes discovered include naïve- (Spic, Scpep1 and Gjb5) and primed-associated (Sema6a and Jakmip2) genes as well as naïve-to primed transition genes (Dusp6 and Trip6). more...

Organism:

Bos taurus; Sus scrofa; Mus musculus

Type:

Expression profiling by high throughput sequencing

4 related Platforms

34 Samples

Download data: BEDGRAPH, WIG

(Submitter supplied) Activin/Nodal/TGF-β signaling pathway plays a major role in maintaining mouse epiblast stem cells (mEpiSCs). The mEpiSC medium which contains Activin A and bFGF induces differentiation of mouse embryonic stem cells (mESCs) to mEpiSC. Here we show that Activin A also has an ability to efficiently propagate mESCs without differentiation to mEpiSCs when combined with a MEK inhibitor PD0325901. mESCs cultured in Activin+PD retained high-level expression of naive pluripotency-related transcription factors. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

3 Samples

Download data: CEL

(Submitter supplied) The combination of Wnt pathway activation by the GSK3 inhibitor and ERK pathway inhibition by the MEK inhibitor, which is known as 2i is a well-established method to maintain mouse embryonic stem cell (mESC) self-renewal. Here we show that Activin A also has the ability to promote naive pluripotency of mESCs when combined with the MEK inhibitor PD0325901. mESCs were efficiently propagated in a medium containing both Activin A and the MEK inhibitor (PD0325901). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

6 Samples

Download data: CEL

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

Organism:

Mus musculus

Type:

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

Platform:

GPL19057

57 Samples

Download data: BED, TXT

(Submitter supplied) Tet-enzyme-mediated 5-hydroxymethylation of cytosine in DNA plays a crucial role in mouse embryonic stem cells (ESCs). In RNA also, 5-hydroxymethylcytosine (5hmC) has recently been evidenced, but its physiological roles are still largely unknown. Here we show the contribution and function of this mark in mouse ESCs and differentiating embryoid bodies. Transcriptome-wide mapping in ESCs revealed hundreds of messenger RNAs marked by 5hmC at sites characterized by a defined unique consensus sequence and particular features. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19057

26 Samples

Download data: BED