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Links from GEO DataSets

Items: 20

1.

Delineation of EZH2 oncogenic functions in hepatocellular carcinoma

(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
Series
Accession:
GSE17733
ID:
200017733
2.

Expression analysis of sk-hep-1(sk) cell and sk-hep-1-sh EZH2(sks) cell

(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
Series
Accession:
GSE68863
ID:
200068863
3.

Genome-wide maps of H3K27me3 modification sites in sk-hep-1,sk-hep-1-shEZH2 and LO2 cells.

(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
Series
Accession:
GSE68758
ID:
200068758
4.

Hepatoma cell lines vs. Universal control 3

(Submitter supplied) Gene expression profiles in hepatoma cells Keywords: Cell type comparison
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL2913
36 Samples
Download data
Series
Accession:
GSE3536
ID:
200003536
5.

Hepatoma cell lines vs. Universal control 2

(Submitter supplied) Gene expression profiles in hepatoma cells Keywords: Cell type comparison
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL2912
18 Samples
Download data
Series
Accession:
GSE3511
ID:
200003511
6.

Hepatoma cell lines vs. Universal control

(Submitter supplied) Gene expression profiles in hepatoma cells Keywords: Cell type comparison
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL2911
18 Samples
Download data
Series
Accession:
GSE3444
ID:
200003444
7.

A cDNA microarray analysis was performed on shRNA KDs of EZH2, SUZ12, BMI1, or CBX8 HepG2 cells.

(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
Series
Accession:
GSE54108
ID:
200054108
8.

Chip-chip from HepG2 cells with EZH2, SUZ12 and H3K27me3

(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
Series
Accession:
GSE52300
ID:
200052300
9.

Comparison of TCF hyper-activated and control Huh7 cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by array; Expression profiling by SAGE
Platforms:
GPL570 GPL4
8 Samples
Download data: CEL, TAR
Series
Accession:
GSE11956
ID:
200011956
10.

H3K27 Methyltransferase PRC2 Represses Wnt Genes to Facilitate Adipogenesis

(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
Series
Accession:
GSE20054
ID:
200020054
11.
Full record GDS3765

Histone H3K27 methyltransferase Ezh2 deletion effect on primary preadipocyte cultures

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
12.

Affymetrix SNP array data for EZH2 mediated gene copy number change in breast tumor initiating cells

(Submitter supplied) EZH2 is shown to be involved in regulation of DNA damage repair which may contribute to development of breast tumor initiating cells. To identify genomic aberrations regulated by EZH2 expression, we performed genome wide copy number variation analysis in breast tumor initiating cells expressing EZH2 compared to the vector control. This finding suggests EZH2 contributes to oncogenic amplification in breast tumor initiating cells.
Organism:
Homo sapiens
Type:
Genome variation profiling by SNP array; SNP genotyping by SNP array
Platform:
GPL6801
6 Samples
Download data: CEL, CHP
Series
Accession:
GSE24144
ID:
200024144
13.

Oncogenic Serine-Threonine Kinase Receptor Associated Protein Supports Hepatocellular Carcinoma Cell Growth by Enhancing Wnt/β-catenin Signaling

(Submitter supplied) Serine-threonine kinase receptor-associated protein (STRAP) is upregulated in breast, colorectal and lung cancers, promoting their growth. We identify the upregulation of STRAP in hepatocellular carcinomas. Elevated STRAP endows tumor cells with growth advantage by reprograming a variety of metabolic processes and signaling pathways critical for hepatocellular carcinoma progression. Especially, enhanced Wnt/β-catenin signaling is likely to be a major effector of its tumor-promoting role.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
12 Samples
Download data: XLSX
Series
Accession:
GSE101061
ID:
200101061
14.

Global analysis of genes regulated by canonical Wnt pathway

(Submitter supplied) Up-regulation of canonical Wnt signaling has been implicated in liver fibrosis and cancer. To determine canonical Wnt target genes potentially implicated in these diseases, we performed microarray analysis of culture-activated rat hepatic stellate cells (HSCs) treated with canonical Wnt inhibitors, DKK-1, ICG-001, or FJ9.
Organism:
Rattus norvegicus albus; Rattus norvegicus
Type:
Expression profiling by array
Platform:
GPL6247
6 Samples
Download data: CEL
Series
Accession:
GSE76330
ID:
200076330
15.

mRNA expression after siRNA-mediated knock down of Enhancer of zeste homolog 2 (Ezh2) in human umbilical vein endothelial cells

(Submitter supplied) mRNA expression after Ezh2 knock down was analyzed to identify genes regulated by Ezh2.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL6480
3 Samples
Download data: TXT
Series
Accession:
GSE41610
ID:
200041610
16.

Supraorbital cranial mesenchyme with ectoderm upon the deletion of β-catenin

(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
Platforms:
GPL17021 GPL19057
10 Samples
Download data: BW
Series
Accession:
GSE96872
ID:
200096872
17.

Gene expression changes in the supraorbital cranial mesenchyme after beta-catenin deletion in vivo

(Submitter supplied) Goal of this study was to examine gene expression changes upon conditional deletion of beta-catenin at e13.5 cranial mesenchyme.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
7 Samples
Download data: TXT, XLSX
Series
Accession:
GSE96871
ID:
200096871
18.

H3K27me3 enrichment in the supraorbital cranial mesenchyme with ectoderm upon the deletion of β-catenin

(Submitter supplied) H3K27me3 enrichment in the supraorbital cranial mesenchyme with ectoderm upon the deletion of β-catenin
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
3 Samples
Download data: BW
Series
Accession:
GSE96604
ID:
200096604
19.

Gene expression changes in dorsal dermal fibroblasts after beta-catenin deletion in vivo

(Submitter supplied) Goal of this study was to examine gene expression changes upon conditional deletion of beta-catenin at E10.5 in dermal fibroblasts. Method: Skin tissues were treated in 0/25% trypsin for 15 min at 37 degrees C to obtain single cells for FACS sorting and collected in RNA later. RNA was extracted with Karcturus pico pure kit. The RT and amplification was done using Nugen's ovation RNA-seq system V2. Libraries for sequencing were prepared with Illumina TruSeq kit. Transcriptome of FACS sorted E13.5 Engrailed1; RRYFP lineage-marked dorsal dermal fibroblasts was generated next-gen sequencing, in triplicate, using Illumina HiSeq machine. The sequence reads that passed quality filters were analyzed by TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: We mapped about 33-49 million sequence reads per sample and obtained 76-79% of uniquely mapped percentage. We assembled the reads to the mouse ref genome (build mm10).
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
5 Samples
Download data: XLSX
Series
Accession:
GSE75944
ID:
200075944
20.

Gene expression analysis in human colon cancer cells and liver cancer cells with FoxA knockdown.

(Submitter supplied) FoxA transcription factors are involved in development and tumorigenesis of the gastrointestinal tract. However, the downstream programs controlled by FoxA factors remain poorly understood. The goal of this study is to understand the transcriptional responses regulated by FoxA proteins in liver and colon cancer cells.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL6244
12 Samples
Download data: CEL
Series
Accession:
GSE46466
ID:
200046466
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