GEO DataSets

(Submitter supplied) Investigation of EZH2 knocking down on whole genome gene expression level changes in sk-hep-1 compared to sk-hep-1-sh EZH2.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL18943

2 Samples

Download data: CALLS, PAIR

(Submitter supplied) We report the application of chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) for high-throughput profiling of H3K27me3 modifications in sk-hep-1(sk), sk-hep-1-shEZH2 (sks) and LO2 cells. Following standard ChIP procedure, 10 ng of each DNA sample was used for Illumina sequencing. Statistically significant ChIP-enriched regions (peaks) were identified by sk vs sks (p-value threshold of 10-2) or sk vs LO2 (p-value threshold of 10-3). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

3 Samples

Download data: BED, WIG, XLS

(Submitter supplied) The goal of this study was to delineate the important EZH2 direct target genes that mediate the oncogenic properties of EZH2 in HCC. The EZH2 direct target genes in two HCC cell lines were identified by chromatin immunoprecipitation microarray (ChIP-chip) analysis and later confirmed by independent ChIP-PCR. The functions of the target genes were further examined.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL4125 GPL4124

8 Samples

Download data: TXT

(Submitter supplied) Genomic sequencing of hepatocellular carcinoma (HCC) uncovers a paucity of actionable mutations, underscoring the necessity to exploit epigenetic vulnerabilities for therapeutics. In HCC, EZH2-mediated H3K27me3 represents a major oncogenic chromatin modification, but how it modulates the therapeutic vulnerability of signaling pathways remains unknown. Here, we identified that EZH2 maintains H3K27 methylome through epigenetic silencing of specific gene sets. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18480

10 Samples

Download data: BW

(Submitter supplied) Polycomb group (PcG) proteins including EZH2, SUZ12 ,BMI1,CBX8 and so on, which specifically catalyze trimethylation of histone 3 lysine 27 (H3K27me3), and methylated H3K27 can be recognized by other specific binding proteins to compress chromatin structure, leading to the transcriptional repression of the target genes. To explore a potential functional implication of PcG components in HCC, we stably transfected HepG2 cells with either vectors or constructs expressing shRNA that specifically targets EZH2, SUZ12, BMI1, or CBX8. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10332

5 Samples

Download data: TXT

(Submitter supplied) Polycomb group (PcG) proteins including EZH2, SUZ12 and so on, which specifically catalyze trimethylation of histone 3 lysine 27 (H3K27me3), and methylated H3K27 can be recognized by other specific binding proteins to compress chromatin structure, leading to the transcriptional repression of the target genes. To completely understand the epigenetic profile and molecular network of PcG in HCC, we performed ChIP-on-chip screens with EZH2, SUZ12 and H3K27me3 antibodies in HepG2 cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL9448

3 Samples

Download data: GFF, JPG, PAIR, XLSX

(Submitter supplied) Although many protein-coding genes have been identified to be aberrantly expressed in hepatocellular carcinoma (HCC), the mechanisms that account for development and progression of HCC remain unclear. In recent years, long noncoding RNAs (lncRNAs) have been shown to have critical regulatory roles in mammalian cell biology. Many lncRNAs can result in aberrant expression of gene products that may contribute to cancer biology. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by genome tiling array

Platform:

GPL11269

10 Samples

Download data: PAIR

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

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array; Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL21145

48 Samples

Download data: IDAT

(Submitter supplied) Hepatocellular carcinoma (HCC) is the most common primary liver malignancy with cases increasing dramatically in the USA. Developing more effective targeted therapies for HCC is an urgent need. The FDA-approved DNA methyltransferase inhibitors (DNMTis) 5-azacytidine (5-aza-CR, Vidaza) and 5-aza-2’-deoxycytidine (5-aza-CdR, Decitabine) represented the first clinical breakthrough to target aberrant cancer epigenomes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

24 Samples

Download data: TSV

(Submitter supplied) Hepatocellular carcinoma (HCC) is the most common primary liver malignancy with cases increasing dramatically in the USA. Developing more effective targeted therapies for HCC is an urgent need. The FDA-approved DNA methyltransferase inhibitors (DNMTis) 5-azacytidine (5-aza-CR, Vidaza) and 5-aza-2’-deoxycytidine (5-aza-CdR, Decitabine) represented the first clinical breakthrough to target aberrant cancer epigenomes. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

24 Samples

Download data: IDAT, TXT

(Submitter supplied) Atherosclerosis is a focal disease that preferentially develop in the regions of atheroprone disturbed flow, but less in regions of atheroprotective laminar flow. The mechanisms by which atheroprotective laminar flow prevents atherosclerosis at the epigenetic level remain largely unknown. In this study, we observed that laminar flow decreased histone methyltransferase EZH2, which imposes a repressive epigenetic mark of histone 3 lysine 27 trimethylation (H3K27me3) onto target gene promoters, leading to transcriptional silencing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

10 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL16558 GPL17586

22 Samples

Download data: BED, CEL, TAB

(Submitter supplied) in this study we define an epigenomic profile of PRC2 (H3K27me3 and bivalent) tragets in four newly diagnosed MM patients. Using Oncomine database we demonstarte that PRC2 targets are underexpressed with advanced ISS stages and correlated to poor outcome. Pharmacological inhibition of UNC1999 showed anti-myeloma potential in vitro by activating the expression genes related to apoptosis and cell differenatiation.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

6 Samples

Download data: CEL

(Submitter supplied) Multiple myeloma (MM) is a hematopoietic malignancy characterised by the accumulation of neoplastic post-germinal centre, isotype-switched, long-lived plasma cell within the bone marrow. In genetic and clinical terms MM is highly heterogeneous and remains fatal. Here we present the first epigenomic map of MM derived from freshly isolated bone marrow plasma cells from four patients. Using ChIP- and RNA-sequencing we define a set of silent H3K27me3 targets, active genes bearing H3K4me3, and bivalent genes.

Organism:

Homo sapiens

Type:

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

Platform:

GPL16558

16 Samples

Download data: BED, TAB

(Submitter supplied) To identify genes whose expression was suppressed by EZH2, we performed gene expression microarray analysis in control and EZH2 knockdown human SKOV3 EOC cells. Two individual short hairpin RNAs to the human EZH2 gene (shEZH2) were used to limit potential off-target effects.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

9 Samples

Download data: TXT

(Submitter supplied) The Wnt/b-catenin signaling inhibits adipogenesis. Genome-wide profiling studies have revealed the enrichment of histone H3K27 methyltransferase PRC2 on Wnt genes. However, the functional significance of such a direct link between the two types of developmental regulators in mammalian cells, and the role of PRC2 in adipogenesis, remain unclear. Here we show PRC2 and its H3K27 methyltransferase activity are required for adipogenesis. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS3765

Platform:

GPL1261

4 Samples

Download data: CEL

Analysis of preadipocytes deficient in Ezh2, the enzymatic subunit of H3K27 methyltransferase PRC2. Deletion of Ezh2 eliminates H3K27me3 on Wnt promoters leading to activation of Wnt/b-catenin signaling and inhibition of adipogenesis. Results provide insight into the role of PRC2 in adipogenesis.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 genotype/variation sets

Platform:

GPL1261

Series:

GSE20054

4 Samples

Download data: CEL

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

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

18 Samples

Download data: BEDGRAPH

(Submitter supplied) During mesenchymal stem cell (MSC) differentiation, both Wnt signaling and the development of a rigid cytoskeleton promote commitment to the osteoblastic over adipogenic lineage. β-catenin is thought to play a critical role in Wnt effects. We show that β-catenin was additive with cytoskeletal signals to prevent adipogenesis, and β-catenin knockdown promoted adipogenesis even when the actin cytoskeleton was depolymerized. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

9 Samples

Download data: TSV

(Submitter supplied) ChIP-seq of beta-catenin and TCF4 in mouse marrow derived MSCs

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

9 Samples

Download data: BEDGRAPH