GEO DataSets

(Submitter supplied) To study the function of Paf1C in mouse ESCs, we generated an ES cell line stably expressing a location and affinity purification (LAP)-tagged Ctr9 fusiuon protein using the bacterial astificial chromosome (BAC)-based TransgeneOmics approach. To investigate whether pluripotency and lineage control genes differentially regulated upon Paf1C depletion are direct targets of the Paf1C, we analyzed the binding of the Ctr9-LAP fusion protein by ChIP-chip and identified 2175 promoter regions that were bound by Ctr9. more...

Organism:

Mus musculus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL5811

1 Sample

Download data: BED, CEL

(Submitter supplied) To monitor global transcript changes after Paf1C depletion we transfected ESCs with esiRNA targeting Ctr9 and control esiRNA (Luc).

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

8 Samples

Download data: CEL

(Submitter supplied) The relationship between chromatin organization and transcriptional regulation is an area of intense investigation. We have characterized the spatial relationships between alleles of the Oct4, Sox2, and Nanog genes in single cells during the earliest stages of mouse embryonic stem cell (ESC) differentiation and during embryonic development. We describe homologous pairing of the Oct4 alleles during ESC differentiation and embryogenesis, and present evidence that pairing is correlated with the kinetics of ESC differentiation. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL16417

24 Samples

Download data: FA, TXT

(Submitter supplied) Eed (embryonic ectoderm development) is a core component of the Polycomb Repressive Complex 2 (PRC2) which catalyzes the methylation of histone H3 lysine 27 (H3K27). Trimethylated H3K27 (H3K27me3) can act as a signal for PRC1 recruitment in the process of gene silencing and chromatin condensation. Previous studies with Eed KO ESCs revealed a failure to down-regulate a limited list of pluripotency factors in differentiating ESCs. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

24 Samples

Download data: CEL

(Submitter supplied) We have generated iPS cell lines with constitutive Oct4 expression at ES-cell level or 3 times lower. The aim of the experiment was to compare the global gene expression profile between these two cell lines and also between each of them and wild type ES cells.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

6 Samples

Download data: TXT

(Submitter supplied) A) We profiled gene expression changes during ES cell differentiation B) We profiled gene expression changes when Pou5f1 or Nanog is knockdown upon RNAi Keywords: Array Based

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS1824

Platforms:

GPL1261 GPL3440

32 Samples

Download data: CEL, GPR

Analysis of embryonic stem (ES) cells following RNA interference-mediated depletion of Nanog or Oct4. Nanog and Oct4 are required to maintain the pluripotency and self-renewal of ES cells. Differentially expressed genes scanned for the presence of binding sites for Nanog and Oct4.

Organism:

Mus musculus

Type:

Expression profiling by array, transformed count, 3 protocol sets

Platform:

GPL1261

Series:

GSE4189

14 Samples

Download data: CEL

(Submitter supplied) Global gene expression effects of silencing Jmjd1a and Jmjd2c genes We used microarrays to detail the global programme of gene expression after silencing Jmjd1a gene and Jmjd2c gene separately Keywords: dose response

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS3037

Platform:

GPL4234

12 Samples

Download data: JPG, XML

Analysis of embryonic stem (ES) cells following depletion of the histone H3 Lys 9 demethylase genes, Jmjd1a and Jmjd2c. Pluripotent ES cells possess the ability to self-renew indefinitely. Results provide insight into the role of Jmjd1a and Jmjd2c in the maintenance of self-renewal in ES cells.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 3 protocol sets

Platform:

GPL4234

Series:

GSE8937

12 Samples

Download data: JPG, XML

(Submitter supplied) Core circuits of transcription factors stabilize stem and progenitor cells by suppressing genes required for differentiation. We do not know how such core circuits are reorganized during cell fate transitions to allow differentiation and lineage choice to proceed. Here, we asked how the pluripotency circuit, a core transcriptional circuit that maintains mouse embryonic stem (ES) cells in a pluripotent state, is dismantled as ES cells differentiate and choose between the neural ectodermal and mesendodermal progenitor cell fates. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

5 Samples

Download data: TXT

(Submitter supplied) Sustained expression of the key pluripotency transcriptional regulators and proliferative factors is needed for the maintenance of embryonic stem cells and early progenitors of various lineages. Zic3 is one of those factors which has been shown to be important for embryonic stem cell pluripotency. Through combinatorial analysis of transcription factor binding sites and the corresponding gene-regulation, we show that Zic3 not only activates key pluripotency genes but also acts cooperatively with them in connecting important circuits of regulation in ES cell in proliferation and maintenance of early progenitors. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

2 Samples

Download data: BED, TXT

(Submitter supplied) The transcription factor Zic3 is required for maintenance of embryonic stem (ES) cell pluripotency (Lim LS et al, Mol Biol Cell. 2007;18:1348-1358). By genome-wide chromatin immunoprecipitation (ChIP-chip) in ES cells, we have identified 379 direct Zic3 targets, many of which are functionally associated with pluripotency, cell cycle, proliferation, oncogenesis and early embryogenesis.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL4129 GPL4128

2 Samples

Download data: TXT

(Submitter supplied) ChIP-seq based determination of CTCF binding sites in embryonic stem cells (ESC)

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

2 Samples

Download data: BED

(Submitter supplied) Embryonic stem cells (ESCs) cells run a self-renewal gene expression program, requiring the expression of certain transcription factors accompanied by a particular chromosome organization to maintain a balance between pluripotency and the capacity for rapid differentiation. However, how transcriptional regulation is linked to chromosome organization in ESCs remains enigmatic. Here we show that Cohesin exhibits a functional role in maintaining ESC identity through association with the pluripotency transcriptional network. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL1261 GPL9250

14 Samples

Download data: BED, CEL

(Submitter supplied) ChIP-seq based determination of Rad21 binding sites in embryonic stem cells (ESC) and ESC derived Embryoid Bodies (EB) identified

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

4 Samples

Download data: BED

(Submitter supplied) The Cohesin complex has recently been described to regulate gene expression. We wanted to determine the gene expression profile specific in mouse ES cells after depletion of the Cohesin subunit Rad21. We used microarrays to detail the global programme of gene expression underlying depletion of Rad21 and identified distinct early development related genes up-regulated and many pluripotency related genes downregulated.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

8 Samples

Download data: CEL

(Submitter supplied) We report the application of enyzme-based 4C-Seq technique for exploring Pou5f1 enhancer interactome in mouse ES cells.

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

2 Samples

Download data: BED

(Submitter supplied) Landmark events occur in a coordinated manner during preimplantation development of the mammalian embryo, yet the regulatory network that orchestrates these events remains largely unknown. We delineated the regulons of Oct4, Sall4, and Nanog using morpholino (MO)-mediated gene knockdowns followed by microarray analysis of pooled embryos.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

42 Samples

Download data: CEL

(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