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Items: 1 to 20 of 32

1.

Super-enhancer subregions highly bound by the nuclear receptor ESRRB regulate the exit from naïve pluripotency

(Submitter supplied) This study focuses on superenhancers, and includes 1 WGBS profile of EpiSCs.
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL13112
1 Sample
Download data: BED
Series
Accession:
GSE124476
ID:
200124476
2.

Enhancer profiling in Esrrb-/- ES cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
Platform:
GPL19057
21 Samples
Download data: BEDGRAPH
Series
Accession:
GSE139189
ID:
200139189
3.

Enhancer profiling in Esrrb-/- ES cells [4C-seq]

(Submitter supplied) We uncover a pivotal role for ESRRB in demarcating ESC-specific enhancer units, and propose that ESRRB’s developmentally-regulated extinction precipitates their decommissioning with impact on the rewiring of the pluripotency transcriptional programme upon embryo implantation.
Organism:
Mus musculus
Type:
Other
Platform:
GPL19057
9 Samples
Download data: BEDGRAPH
4.

Enhancer profiling in Esrrb-/- ES cells [ChIP-seq]

(Submitter supplied) We uncover a pivotal role for ESRRB in demarcating ESC-specific enhancer units, and propose that ESRRB’s developmentally-regulated extinction precipitates their decommissioning with impact on the rewiring of the pluripotency transcriptional programme upon embryo implantation
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
12 Samples
Download data: BED
Series
Accession:
GSE129179
ID:
200129179
5.

Critical role for P53 in regulating the cell cycle of ground state embryonic stem cells

(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:
GPL13112
19 Samples
Download data: BW
Series
Accession:
GSE141179
ID:
200141179
6.

Critical role for P53 in regulating the cell cycle of ground state embryonic stem cells [RNA-seq]

(Submitter supplied) Mouse Embryonic Stem Cells (ESCs) grown in serum-supplemented conditions are characterized by an extremely short G1-phase due to the lack of G1-phase control. Concordantly, the G1-phase-specific P53-P21 pathway is compromised in serum ESCs. Here we provide evidence that P53 is activated upon transition of serum ESCs to their pluripotent ground state using serum-free 2i conditions and modulates G1-phase progression. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
12 Samples
Download data: TXT
Series
Accession:
GSE141178
ID:
200141178
7.

Critical role for P53 in regulating the cell cycle of ground state embryonic stem cells [ChIP-seq]

(Submitter supplied) Mouse Embryonic Stem Cells (ESCs) grown in serum-supplemented conditions are characterized by an extremely short G1-phase due to the lack of G1-phase control. Concordantly, the G1-phase-specific P53-P21 pathway is compromised in serum ESCs. Here we provide evidence that P53 is activated upon transition of serum ESCs to their pluripotent ground state using serum-free 2i conditions and modulates G1-phase progression. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
7 Samples
Download data: BW
Series
Accession:
GSE141177
ID:
200141177
8.

Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency. (4C-seq)

(Submitter supplied) The mechanisms underlying enhancer activation and the extent to which enhancer-promoter rewiring contributes to spatiotemporal gene expression are not well understood. Using integrative and time resolved analyses we show that the extensive transcriptome and epigenome resetting during the conversion between ‘serum-’ and ‘2i’-states of mouse embryonic stem cells (ESCs) takes place with minimal enhancer-promoter rewiring that becomes more evident in primed-state pluripotency. more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL19057
94 Samples
Download data: BEDGRAPH, BW
Series
Accession:
GSE113750
ID:
200113750
9.

Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency.

(Submitter supplied) The mechanisms underlying enhancer activation and the extent to which enhancer-promoter rewiring contributes to spatiotemporal gene expression are not well understood. Using integrative and time resolved analyses we show that the extensive transcriptome and epigenome resetting during the conversion between ‘serum-’ and ‘2i’-states of mouse embryonic stem cells (ESCs) takes place with minimal enhancer-promoter rewiring that becomes more evident in primed-state pluripotency. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms:
GPL19057 GPL13112
194 Samples
Download data: BEDGRAPH, BIGWIG, BW
Series
Accession:
GSE92412
ID:
200092412
10.

Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency. (ATAC-seq)

(Submitter supplied) The mechanisms underlying enhancer activation and the extent to which enhancer-promoter rewiring contributes to spatiotemporal gene expression are not well understood. Using integrative and time resolved analyses we show that the extensive transcriptome and epigenome resetting during the conversion between ‘serum-’ and ‘2i’-states of mouse embryonic stem cells (ESCs) takes place with minimal enhancer-promoter rewiring that becomes more evident in primed-state pluripotency. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
23 Samples
Download data: BW
Series
Accession:
GSE92411
ID:
200092411
11.

Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency. (ChIP-seq)

(Submitter supplied) The mechanisms underlying enhancer activation and the extent to which enhancer-promoter rewiring contributes to spatiotemporal gene expression are not well understood. Using integrative and time resolved analyses we show that the extensive transcriptome and epigenome resetting during the conversion between ‘serum-’ and ‘2i’-states of mouse embryonic stem cells (ESCs) takes place with minimal enhancer-promoter rewiring that becomes more evident in primed-state pluripotency. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL19057 GPL13112
61 Samples
Download data: BEDGRAPH, BIGWIG, BW
Series
Accession:
GSE92407
ID:
200092407
12.

Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency. (RNA-seq)

(Submitter supplied) The mechanisms underlying enhancer activation and the extent to which enhancer-promoter rewiring contributes to spatiotemporal gene expression are not well understood. Using integrative and time resolved analyses we show that the extensive transcriptome and epigenome resetting during the conversion between ‘serum-’ and ‘2i’-states of mouse embryonic stem cells (ESCs) takes place with minimal enhancer-promoter rewiring that becomes more evident in primed-state pluripotency. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
16 Samples
Download data: BW
Series
Accession:
GSE92403
ID:
200092403
13.

Allele-specific expression profiling of imprinted genes in mouse isogenic pluripotent tissues and cell lines

(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:
GPL19057 GPL11002 GPL13112
22 Samples
Download data: WIG
Series
Accession:
GSE101292
ID:
200101292
14.

Integrative Proteomic Profiling Reveals PRC2-Dependent Epigenetic Crosstalk Maintains Ground-State Pluripotency.

(Submitter supplied) The pluripotent ground state is defined as a basal state free of epigenetic restrictions, which influence lineage specification. While naive embryonic stem cells (ESCs) can be maintained in a hypomethylated state with open chromatin when grown using two small-molecule inhibitors (2i)/leukemia inhibitory factor (LIF), in contrast to serum/LIF-grown ESCs that resemble early post-implantation embryos, broader features of the ground-state pluripotent epigenome are not well understood. 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
Platforms:
GPL19057 GPL13112
19 Samples
Download data: BED, BW
Series
Accession:
GSE101675
ID:
200101675
15.

Mammalian embryo comparison identifies novel pluripotency genes associated with the naïve or primed state

(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:
Sus scrofa; Bos taurus; Mus musculus
Type:
Expression profiling by high throughput sequencing
4 related Platforms
34 Samples
Download data: BEDGRAPH, WIG
Series
Accession:
GSE53387
ID:
200053387
16.

MTF2 recruits Polycomb Repressive Complex 2 by helical shape-selective DNA binding

(Submitter supplied) Polycomb repression of gene expression is essential for development, with a pivotal role played by trimethylation of histone H3 lysine 27 (H3K27me3) that is deposited by Polycomb Repressive Complex 2 (PRC2). The mechanism by which PRC2 is recruited to target genes has remained largely elusive, in particular in vertebrates. Here we demonstrate that MTF2, one of the three vertebrate homologs of Drosophila Polycomblike, is a DNA-binding, methylation-sensitive PRC2 recruiter in mouse embryonic stem cells. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
22 Samples
Download data: BED, BW
Series
Accession:
GSE94300
ID:
200094300
17.

An efficient method for generation of bi-allelic null mutant mouse embryonic stem cell lines and its application for investigating epigenetic modifiers

(Submitter supplied) Mouse embryonic stem (ES) cells are a popular model system to study biological processes, though uncovering recessive phenotypes requires inactivating both alleles. Building upon resources from the International Knockout Mouse Consortium (IKMC), we developed a targeting vector for second allele inactivation in conditional-ready IKMC ‘knockout-first’ ES cell lines. We applied our technology to several epigenetic regulators, recovering bi-allelic targeted clones with a high efficiency of 60%, and used Flp recombinase to restore expression in two null cell lines to demonstrate how our system confirms causality through mutant phenotype reversion. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL11002
8 Samples
Download data: BED, WIG
Series
Accession:
GSE31777
ID:
200031777
18.

Tracking the embryonic stem cell transition from ground state pluripotency

(Submitter supplied) Mouse embryonic stem (ES) cells are locked into self-renewal by shielding from inductive cues. Release from this ground state in minimal conditions offers a system for delineating developmental progression from naive pluripotency. Here we examined the initial transition process. The ES cell population behaves asynchronously. We therefore exploited a short-half-life Rex1::GFP reporter to isolate cells either side of exit from naive status. more...
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL13112
12 Samples
Download data: TXT
Series
Accession:
GSE92273
ID:
200092273
19.

Systematic in vitro and in vivo characterization of Leukemia-inhibiting factor (LIF)- and Fibroblast growth factor (FGF) -derived porcine induced pluripotent stem cells (piPSC) vs. embryonic stages

(Submitter supplied) Systematic in vitro and in vivo characterization of Leukemia-inhibiting factor (LIF)- and Fibroblast growth factor (FGF) -derived porcine induced pluripotent stem cells (Cell reprogramming -basic developmental studies in the pig) vs Porcine embryonic stages (Plurisys) Global gene expression analyses and comparisons of LIF piPSC, FGF piPSC, Parental fibroblast line day 7-8 porcine embryo, day 10-11 porcine embryo, day 12-13 porcine embryo. more...
Organism:
Sus scrofa
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11429
18 Samples
Download data: TXT
Series
Accession:
GSE92889
ID:
200092889
20.

Dynamics of gene silencing during X inactivation using allele-specific RNA-Seq

(Submitter supplied) Background: During early embryonic development, one of the two X chromosomes in mammalian female cells is inactivated to compensate for a potential imbalance in transcript levels with male cells containing a single X chromosome. We use mouse female Embryonic Stem Cells (ESCs) with nonrandom XCI and polymorphic X chromosomes to study the dynamics of gene silencing over the inactive X chromosome (Xi) by high-resolution allele-specific RNA-Seq. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL19057 GPL13112 GPL11002
20 Samples
Download data: BED, TXT, WIG
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