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Items: 1 to 20 of 44

1.

A plug and play microfluidic platform for standardized sensitive low-input Chromatin Immunoprecipitation

(Submitter supplied) Epigenetic profiling by chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become a powerful tool for genome-wide identification of regulatory elements, for defining transcriptional regulatory networks and for screening for biomarkers. However, the ChIP-seq protocol for low-input samples is laborious, time-consuming and suffers from experimental variation, resulting in poor reproducibility and low throughput. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
51 Samples
Download data: BW, WIG
Series
Accession:
GSE120673
ID:
200120673
2.

STARR-seq identifies chromatin masked enhancers in pluripotent mouse embryonic stem cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
30 Samples
Download data: BW
Series
Accession:
GSE143546
ID:
200143546
3.

STARR-seq identifies chromatin masked enhancers in pluripotent mouse embryonic stem cells [single_cell_RNA-Seq]

(Submitter supplied) Enhancers are distal regulators of gene expression that shape cell identity and regulate cell fate transitions. Mouse embryonic stem cells (mESCs) are a typical example of cells whose pluripotent identity is maintained by a complex enhancer landscape, that is drastically altered upon differentiation. Genome-wide chromatin accessibility and histone modification assays are commonly used as a proxy for enhancer location, strength and dynamics. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
6 Samples
Download data: BW, TSV, TXT
Series
Accession:
GSE143545
ID:
200143545
4.

STARR-seq enhancer activity in mouse embryonic stem cells cultured in 2i+LIF or serum+LIF [STARR-seq]

(Submitter supplied) Enhancers are distal regulators of gene expression that shape cell identity and regulate cell fate transitions. Mouse embryonic stem cells (mESCs) are a typical example of cells whose pluripotent identity is maintained by a complex enhancer landscape, that is drastically altered upon differentiation. Genome-wide chromatin accessibility and histone modification assays are commonly used as a proxy for enhancer location, strength and dynamics. more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL19057
8 Samples
Download data: BW, TSV
5.

STARR-seq identifies chromatin masked enhancers in pluripotent mouse embryonic stem cells [RNA-Seq]

(Submitter supplied) Enhancers are distal regulators of gene expression that shape cell identity and regulate cell fate transitions. Mouse embryonic stem cells (mESCs) are a typical example of cells whose pluripotent identity is maintained by a complex enhancer landscape, that is drastically altered upon differentiation. Genome-wide chromatin accessibility and histone modification assays are commonly used as a proxy for enhancer location, strength and dynamics. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
12 Samples
Download data: BW, TSV
Series
Accession:
GSE143543
ID:
200143543
6.

STARR-seq identifies chromatin masked enhancers in pluripotent mouse embryonic stem cells [ChIP-seq]

(Submitter supplied) Enhancers are distal regulators of gene expression that shape cell identity and regulate cell fate transitions. Mouse embryonic stem cells (mESCs) are a typical example of cells whose pluripotent identity is maintained by a complex enhancer landscape, that is drastically altered upon differentiation. Genome-wide chromatin accessibility and histone modification assays are commonly used as a proxy for enhancer location, strength and dynamics. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
4 Samples
Download data: BW, TSV
Series
Accession:
GSE143541
ID:
200143541
7.

Two distinct functional axes of positive feedback-enforced PRC2 recruitment in mouse embryonic stem cells

(Submitter supplied) Polycomb Repressive Complex 2 (PRC2) plays an essential role in gene repression during development, catalysing H3 lysine 27 trimethylation (H3K27me3). MTF2 in the PRC2.1 sub-complex, and JARID2 in PRC2.2, are central in core PRC2 recruitment to target genes in mouse embryonic stem cells (mESCs). To investigate how PRC2.1 and PRC2.2 cooperate, we combined Polycomb mutant mESCs with chemical inhibition of binding to H3K27me3. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
69 Samples
Download data: BAM
Series
Accession:
GSE133085
ID:
200133085
8.

In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. SubSeries GSE105762 contains bulk RNA-Seq data, while SubSeries GSE145726 contains single-cell RNA-Seq data.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL19057 GPL17021
23 Samples
Download data: TXT
Series
Accession:
GSE145727
ID:
200145727
9.

In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states (II, single-cell RNA-Seq data)

(Submitter supplied) Naive pluripotent cells in the implanting mouse blastocyst generate a rosette structure before undergoing lumenogenesis to form the egg cylinder. Simultaneously, they acquire primed pluripotency, the ability to differentiate into the primary germ layers. The existence of discrete intermediate pluripotent states during this transition has not been demonstrated. We identify here a distinct rosette pluripotent state, defined by co-expression of naive factors with transcription factor OTX2. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
6 Samples
Download data: TXT
Series
Accession:
GSE145726
ID:
200145726
10.

In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states

(Submitter supplied) Upon implantation, the naive pluripotent epiblast of the mouse blastocyst generates a rosette, undergoes lumenogenesis and forms the primed pluripotent egg cylinder, able to generate the embryonic tissues. How pluripotency progression and morphogenesis are linked, and whether intermediate pluripotent states exist remain controversial. We identify here a rosette pluripotent state, defined by co-expression of naive factors with transcription factor OTX2. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
4 Samples
Download data: BED, BW
Series
Accession:
GSE112234
ID:
200112234
11.

In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states (I, bulk RNA-Seq data)

(Submitter supplied) Naive pluripotent cells in the implanting mouse blastocyst generate a rosette structure before undergoing lumenogenesis to form the egg cylinder. Simultaneously, they acquire primed pluripotency, the ability to differentiate into the primary germ layers. The existence of discrete intermediate pluripotent states during this transition has not been demonstrated. We identify here a distinct rosette pluripotent state, defined by co-expression of naive factors with transcription factor OTX2. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
17 Samples
Download data: TXT, XLSX
Series
Accession:
GSE105762
ID:
200105762
12.

DNA methylation profiling of proliferating and differentiating keratinocytes

(Submitter supplied) The epidermal compartment of the skin is regenerated constantly by proliferation of epidermal keratinocytes. Differentiation of a subset of these keratinocytes allows the epidermis to retain its barrier properties. Regulation of keratinocyte fate – whether to remain proliferative or terminally differentiate – is complex and not fully understood. The objective of our study was to assess if DNA methylation changes contribute to the regulation of keratinocyte fate. more...
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL21145
10 Samples
Download data: IDAT, TXT
Series
Accession:
GSE144669
ID:
200144669
13.

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
14.

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
15.

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
16.

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
17.

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
18.

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
19.

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
20.

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
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