GEO DataSets

Analysis of embryonic stem (ES) cells deleted for BAF250a in vitro. BAF250 is a component of the BAF chromatin remodeling complex. Results provide insight into the role of BAF250a in ES cell self-renewal and differentiation.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 3 genotype/variation sets

Platform:

GPL1261

Series:

GSE10553

4 Samples

Download data: CEL, CHP

(Submitter supplied) To study the function of BAF250 during ES cell self renewal and differentiation Keywords: gene expression comparison between heterozygous,homozygoous and wild type ES cells

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS3387

Platform:

GPL1261

4 Samples

Download data: CEL, CHP

(Submitter supplied) We used BAF250b-/- ES cells, two independently derived clones, at 18 and 72 hr in culture and compared them with parental cell line (wild-type) at the same time in culture (two replications each). Total RNAs were extracted using Trizol (Invitrogen) according to manufacturer protocol. 2.5 ug of total RNA samples were labeled with Cy3-CTP using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4358

12 Samples

Download data: TIFF, TXT

(Submitter supplied) BAF complex is one major group of chromatin remodeling factors in mammals. However, how BAF regulated nucleosomes and other histone modifications is not clear. Here we delete BAF250a, a major component in esBAF to study the nucleosome and histone changes in ESCs. We find that deletion of BAF250a leads to nucleosome occupancy increase in TSS regions and non-pioneer transcription factor binding sites. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

10 Samples

Download data: TXT, WIG

(Submitter supplied) Every known SWI/SNF chromatin-remodeling complex incorporates an ARID DNA binding domain-containing subunit. Despite being a ubiquitous component of the complex, physiological roles for this domain remain undefined. Here we show that disruption of ARID1a-DNA binding in mice results in embryonic lethality, with mutant embryos manifesting prominent defects in the heart and extraembryonic vasculature. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

12 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL16417 GPL4134

24 Samples

Download data: BW, TXT

(Submitter supplied) Embryonic stem cell (ESC) self-renewal and pluripotency is controlled by the coordinated action of transcription factors and chromatin regulators. Compared to the pluripotency transcription factors, the function of the chromatin regulators, especially the ATP-dependent chromatin remodelers, remains poorly understood in ESCs. Here, we show that INO80, a SWI/SNF family chromatin remodeling complex, is essential for ESC self-renewal, pluripotency, somatic cell reprogramming, and embryonic development. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4134

10 Samples

Download data: TXT

(Submitter supplied) Embryonic stem cell (ESC) self-renewal and pluripotency is controlled by the coordinated action of transcription factors and chromatin regulators. Compared to the pluripotency transcription factors, the function of the chromatin regulators, especially the ATP-dependent chromatin remodelers, remains poorly understood in ESCs. Here, we show that INO80, a SWI/SNF family chromatin remodeling complex, is essential for ESC self-renewal, pluripotency, somatic cell reprogramming, and embryonic development. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4134

12 Samples

Download data: TXT

(Submitter supplied) Embryonic stem cell (ESC) self-renewal and pluripotency is controlled by the coordinated action of transcription factors and chromatin regulators. Compared to the pluripotency transcription factors, the function of the chromatin regulators, especially the ATP-dependent chromatin remodelers, remains poorly understood in ESCs. Here, we show that INO80, a SWI/SNF family chromatin remodeling complex, is essential for ESC self-renewal, pluripotency, somatic cell reprogramming, and embryonic development. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16417

12 Samples

Download data: BED, BW

(Submitter supplied) Lineage segregation in the mouse embryo is a finely controlled process dependent upon coordination of signalling pathways and transcriptional responses. We employed conditional deletion of Oct4 to investigate consequences of interference with embryonic patterning and lineage specification. Nanog becomes upregulated in the first epiblast cells to lose Oct4, leading to an expanded Nanog-positive domain. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

5 Samples

Download data: TXT

(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:

GPL21103 GPL17021

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) The mammalian SWI/SNF chromatin-remodeling BAF (BRG1/BRM-associated factor) complex has an essential role in developmental and pathological processes. We show that deletion of Baf155 encoding a subunit of the BAF complex in the Tie2(+) lineage (Baf155 CKO) leads to defects in yolk sac myeloid and definitive erythroid (EryD) lineage differentiation from erythromyeloid progenitors (EMPs). The chromatin of myeloid gene loci in Baf155 CKO EMPs is mostly inaccessible and enriched mainly by the ETS binding motif. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

2 Samples

Download data: BIGWIG

(Submitter supplied) Dppa4 (Developmental pluripotency-associated 4) has been identified in several highprofile screens as a gene that is expressed exclusively in pluripotent cells. It encodes a nuclear protein with a SAP-like domain and appears to be associated preferentially with transcriptionally active chromatin. Its exquisite expression pattern and results of RNA interference experiments have led to speculation that Dppa4, as well as its nearby homolog Dppa2, might play essential roles in embryonic stem cell function and/or germ cell development. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

6 Samples

Download data: CEL, CHP

(Submitter supplied) We report here chromatin related factor Whsc1 links pluripotency exit and mesendodermal differentiation. We performed RNA-seqs to compare Whsc1+/+ and Whsc1-/- embryonic stem cells (ESCs) to compare the transcriptomes. UMI-4C experiments have been performed to identify regions having contacts with promoter regions of downstream Whsc1 targets: the mesendoderm transcritpion factors

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL17021 GPL19057

36 Samples

Download data: BW, TXT

(Submitter supplied) Primitive ectoderm cells (PE) in blastocysts represent the foundation of the pluripotent state, which is lost progressively during development. For example, development of epiblast cells from PE in postimplantation embryos is accompanied by transcriptional and epigenetic changes, including DNA methylation and X inactivation (Refs); these changes alter the nature of epiblast cells fundamentally, affecting their responsiveness to signaling molecules, and constitute a robust boundary that prevents their reversion to a PE-like state. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL2995

12 Samples

Download data: TXT

(Submitter supplied) The composition of chromatin remodeling complexes dictates how these enzymes control transcriptional programs and cellular identity. Here, we investigate the composition of SWI/SNF complexes in embryonic stem cells (ESCs). In contrast to differentiated cells, ESCs have a biased incorporation of certain paralogous SWI/SNF subunits, with low levels of Brm, BAF170 and ARID1B. Upon differentiation, the expression of these subunits increases, resulting in a higher diversity of compositionally distinct SWI/SNF enzymes. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL8321

4 Samples

Download data: CEL

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by array

Platforms:

GPL4134 GPL4133

12 Samples

Download data: TXT

(Submitter supplied) BRG1-SWI/SNF complex is an important chromatin remodeling complex that involved in various biological processes. Here we described the genome-wide binding of histone acetylation upon BRG1 depletion in human embryonic stem cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

6 Samples

Download data: TXT