GEO DataSets

(Submitter supplied) Here we report that NONO, a nuclear para-speckle component, instead functions as a chromatin regulator in mESCs acting in the ERK signaling pathway to regulate the balance between ground state versus mESCs primed for differentiation. NONO loss increases a \u201cground-like\u201d population of mESCs favoring self-renewal and more resist to differentiation, partially mimicking the effects of 2i. Mechanistically, NONO and ERK mainly co-binds a subset of development related, bivalent genes. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

11 Samples

Download data: BED, BEDGRAPH

(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

17 Samples

Download data: BED, BEDGRAPH, FPKM_TRACKING

(Submitter supplied) Here we report that Nono instead functions as a chromatin regulator cooperating with Erk to regulate mESC pluripotency. We demonstrate that Nono loss leads to robust self-renewing mESCs with enhanced expression of Nanog and Klf4, epigenome and transcriptome re-patterning to a “ground-like state” with global reduction of H3K27me3 and DNA methylation resembling the Erk inhibitor PD03 treated mESCs and 2i (both GSK and Erk kinase inhibitors)-induced “ground state”. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: FPKM_TRACKING

(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:

GPL11002

11 Samples

Download data: BED, BW

(Submitter supplied) Carrying out both RNA-seq and Smad1/5 genome-wide chromatin immunoprecipitation and sequencing (ChIP-seq) analyses of mESCs in the naïve or primed states, we revisit the roles of BMP signaling in mESCs.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

6 Samples

Download data: BED, BW

(Submitter supplied) Carrying out both RNA-seq and Smad1/5 genome-wide chromatin immunoprecipitation and sequencing (ChIP-seq) analyses of mESCs in the naïve or primed states, we revisit the roles of BMP signaling in mESCs.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

5 Samples

Download data: BW, TXT

(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) Tbx3, a member of the T-box family, plays important roles in development, stem cells, nuclear reprogramming and cancer. Loss of Tbx3 induces differentiation in mouse embryonic stem cells (mESCs). However, we show that mESCs exist in an alternate stable pluripotent state in the absence of Tbx3. In-depth transcriptome analysis of this mESC state reveals Dppa3 as a direct downstream target of Tbx3. Also Tbx3 facilitates the cell fate transition from pluripotent cells to mesoderm progenitors by directly repressing Wnt pathway members required for differentiation. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL13112 GPL9250

53 Samples

Download data: BED, BEDGRAPH, BIGWIG, TXT

(Submitter supplied) We conducted RNA/RNA binding protein immunoprecipitation (RIP) followed by high throughput sequencing to identify mRNA targets of Brf1 (Zfp36l1) and Brf2 (Zfp36l2) in mouse embryonic stem cells. We collected over 190 million sequencing reads and identified many highly enriched protein coding mRNAs. Gene ontology analysis of enriched genes reveals that transcription factors and intercellular signaling proteins account for a large fraction of the targets, many of which are important for pluripotency and differentiation.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: TXT

(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

Platform:

GPL17021

24 Samples

Download data

(Submitter supplied) In this study we determine the profile of DNA methylation by RRBseq of mESC in the absence of Smad1 and Smad5 and in subpopulation of mESC with different levels of BMP-SMAD activation. We observed a general loss of DNA methylation associated with low or absent BMP-SMAD signalling in mESCs.

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: BEDGRAPH

(Submitter supplied) In this study we determine the transcriptional profile by RNAseq of mESC in the absence of Smad1 and Smad5 and in subpopulation of mESC with different levels of BMP-SMAD activation.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: TXT

(Submitter supplied) Mouse embryonic stem cells (mESCs) cultured under serum/LIF conditions exhibit heterogeneous expression of pluripotency-associated factors that can be overcome by two inhibitors (2i) of the MEK and GSK3 pathway, respectively. Several studies have shown that the “ground state” induced by 2i is characterized by global hypomethylation and specific transcriptional profiles, but little is known about the contributing effectors. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

36 Samples

Download data: NARROWPEAK, TDF

(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) 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:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

46 Samples

Download data: BW

(Submitter supplied) Histone acetylation and the acetyl-lysine reader Brd4 have recently been implicated in embryonic stem cell (ESC) proliferation and self-renewal. We found that naïve pluripotent ESCs exhibit increased incorporation of glucose-derived carbons onto acetylated histones and elevations in H3K9ac and Brd4 recruitment at pluripotency gene promoters. Surprisingly, both H3K9 acetyltransferases, GCN5 and PCAF, and Brd4 recruitment were dispensable for proliferation, self-renewal and pluripotency of naïve ESCs. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

12 Samples

Download data: TXT

(Submitter supplied) Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in 46C mouse embryonic stem cells overexpressing PB-Gbx2 or PB empty vector at gene expression level. Results provide important information of the response of up-regulating Gbx2, such as specific mechano-responsive genes, up- or down-regulated genes that were mainly enriched in signaling pathways regulating pluripotency of stem cells

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21493

2 Samples

Download data: TXT

(Submitter supplied) The Wnt/β-catenin signalling pathway is a key regulator of embryonic stem cell self-renewal and differentiation. Constitutive activation of this pathway has been shown to significantly increase mouse embryonic stem cell (mESC) self-renewal and pluripotency marker expression. In this study, we generated a novel β-catenin knock-out model in mESCs by using CRISPR/Cas9 technology to delete putatively functional N-terminally truncated isoforms observed in previous knock-out models. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

8 Samples

Download data: CSV