GEO DataSets

(Submitter supplied) For validating the newly defined PAF, PCGF and TBX3 modules, the major transcriptional factor of each module (Ctr9, Pcgf6 and Tbx3) was knocked down individually by RNAi in a Nanog-GFP reporter ESC line. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at one time points.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: TXT

(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

(Submitter supplied) The transcription factor Oct4 is essential for the maintenance and induction of stem cell pluripotency, but its functional roles are not fully understood. Here, we investigate the functions of Oct4 by depleting and subsequently recovering it in mouse embryonic stem cells and conducting a time-resolved multiomics analysis. Oct4 depletion leads to an immediate loss of its binding to enhancers, accompanied by a decrease in mRNA synthesis from its target genes that are part of the transcriptional network that maintains pluripotency. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL21626 GPL18480

64 Samples

Download data: BW, GTF

(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

(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

(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

(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

(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

(Submitter supplied) We utilized FAIRE-seq to identify accesible chromatin in mouse embryonic-, epiblast-, and neural- stem cells in addition to mouse embryonic fibroblasts. Analysis of these data sets reveal cell type specific chromatin signatures that differentiate naïve and primed pluripotency. Functional analysis of type-specific peaks revealed cell-type specific enhancers.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

10 Samples

Download data: BED, WIG

(Submitter supplied) Myc is a master transcription factor that has been demonstrated to be required for embryonic stem cell (ESC) pluripotency, self-renewal, and inhibition of differentiation. Although recent works identified several Myc-targets in ESC the list of Myc binding sites is largely incomplete due to the low sensitivity and specificity of the antibodies available so far. To systematically identify Myc binding sites in mouse ESCs here we used a stringent streptavidin based genome-wide chromatin immunoprecipitation (ChIP-Seq) of a biotin-tagged Myc (Bio-Myc) as well as a ChIP-Seq of the Myc partner Max. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16173

4 Samples

Download data: BED

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

Organism:

Mus musculus

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL24247

32 Samples

Download data

(Submitter supplied) The integrated stress response (ISR) is critical for cell survival under stress. In response to diverse environmental cues, eIF2αbecomes phosphorylated, engendering a dramatic change in mRNA translation. The activation of ISR plays a pivotal role in the early embryogenesis but the eIF2-dependent translational landscape in pluripotent embryonic stem cells (ESC) is largely unexplored. We employ a multi-omics approachconsisting of ribosome profiling, proteomics, and metabolomics inwild-type(eIF2α+/+)andphosphorylation-deficient mutant eIF2α(eIF2αA/A)mouse ESCs (mESCs) to investigate phosphorylated (p)-eIF2α-dependent translational control of naïve pluripotency. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: CSV

(Submitter supplied) The integrated stress response (ISR) is critical for cell survival under stress. In response to diverse environmental cues, eIF2αbecomes phosphorylated, engendering a dramatic change in mRNA translation. The activation of ISR plays a pivotal role in the early embryogenesis but the eIF2-dependent translational landscape in pluripotent embryonic stem cells (ESC) is largely unexplored. We employ a multi-omics approachconsisting of ribosome profiling, proteomics, and metabolomics inwild-type(eIF2α+/+)andphosphorylation-deficient mutant eIF2α(eIF2αA/A)mouse ESCs (mESCs) to investigate phosphorylated (p)-eIF2α-dependent translational control of naïve pluripotency. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL24247

20 Samples

Download data: CSV

(Submitter supplied) In this study: (1) We have mapped the genome wide binding distribution and enrichment of Rinf/CXXC5 at genes and regulatory regions in mouse ESCs by ChIP-seq using a specific antibody against Rinf. (2) We have examined the role of Rinf in regulation of ESC gene expression programs by performing transcriptomic analysis of Rinf wild type and knockout ESCs by RNA-seq to identify differentially expressed genes. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL17021 GPL19057

21 Samples

Download data: BW, TXT

(Submitter supplied) The objective of this study was to identify how histone modifications are differentially marked at promoter and enhancer elements in hESCs before and after differentiation to understand the regulatory mechanisms that defined pluripotency and early differentiation.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

29 related Platforms

94 Samples

Download data: CEL, GFF, PAIR

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

Organism:

Mus musculus; Homo sapiens

Type:

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

Platforms:

GPL9052 GPL9185

39 Samples

Download data: BW

(Submitter supplied) Gene regulatory networks are pivotal for many biological processes. In mouse embryonic stem cells (mESCs) the transcriptional network can be divided into three functionally distinct modules: Polycomb, Core and Myc. The Polycomb module represses developmental genes, while the Myc module is associated with proliferative functions and its mis-regulation is linked to cancer development. Here, we show that in mESCs the Polycomb Repressive Complex 2 (PRC2) associated protein EPOP (a.k.a C17orf96, esPRC2p48, E130012A19Rik) co-localizes at chromatin with members of the Myc and Polycomb module. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9185

4 Samples

Download data: BW

(Submitter supplied) Gene regulatory networks are pivotal for many biological processes. In mouse embryonic stem cells (mESCs) the transcriptional network can be divided into three functionally distinct modules: Polycomb, Core and Myc. The Polycomb module represses developmental genes, while the Myc module is associated with proliferative functions and its mis-regulation is linked to cancer development. Here, we show that in mESCs the Polycomb Repressive Complex 2 (PRC2) associated protein EPOP (a.k.a C17orf96, esPRC2p48, E130012A19Rik) co-localizes at chromatin with members of the Myc and Polycomb module. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9185

6 Samples

Download data: BW

(Submitter supplied) Gene regulatory networks are pivotal for many biological processes. In mouse embryonic stem cells (mESCs) the transcriptional network can be divided into three functionally distinct modules: Polycomb, Core and Myc. The Polycomb module represses developmental genes, while the Myc module is associated with proliferative functions and its mis-regulation is linked to cancer development. Here, we show that in mESCs the Polycomb Repressive Complex 2 (PRC2) associated protein EPOP (a.k.a C17orf96, esPRC2p48, E130012A19Rik) co-localizes at chromatin with members of the Myc and Polycomb module. more...

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL9185 GPL9052

29 Samples

Download data: BW, TXT

(Submitter supplied) In the mammalian embryo, epiblast cells must exit the naïve state and acquire formative pluripotency. This cell state transition is recapitulated by mouse embryonic stem cells (ESCs), which undergo pluripotency progression in defined conditions in vitro. However, our understanding of the molecular cascades and gene networks involved in the exit from naïve pluripotency remains fragmentary. Here, we employed a combination of genetic screens in haploid ESCs, CRISPR/Cas9 gene disruption, large-scale transcriptomics and computational systems biology to delineate the regulatory circuits governing naïve state exit. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21103 GPL21493

340 Samples

Download data: CSV