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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression change in Skov3 after EZH2 knockdown

ABSTRACT: 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. Two individual short hairpin RNAs to the human EZH2 gene (shEZH2) were used to limit potential off-target effects. Three technical replicates per group were used.

ORGANISM(S): Homo sapiens

SUBMITTER: Michael Slifker

PROVIDER: E-GEOD-31433 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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ALDH1A1 is a novel EZH2 target gene in epithelial ovarian cancer identified by genome-wide approaches.

Li Hua H Bitler Benjamin G BG Vathipadiekal Vinod V Maradeo Marie E ME Slifker Michael M Creasy Caretha L CL Tummino Peter J PJ Cairns Paul P Birrer Michael J MJ Zhang Rugang R

Cancer prevention research (Philadelphia, Pa.) 20111205 3

Epithelial ovarian cancer (EOC) remains the most lethal gynecologic malignancy in the United States. EZH2 silences gene expression through trimethylating lysine 27 on histone H3 (H3K27Me3). EZH2 is often overexpressed in EOC and has been suggested as a target for EOC intervention. However, EZH2 target genes in EOC remain poorly understood. Here, we mapped the genomic loci occupied by EZH2/H3K27Me3 using chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) and globally ...[more]

PMID: 22144423

Similar Datasets

Gene expression change in Skov3 after EZH2 knockdown

Project description: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.

2011-12-12 | GSE31433 | GEO

Comparasion between SKOV3-shRNARELB and SKOV3-shRNALuc

Project description:Analysis of genes differentially expressed in ovarian cancer cells with sirna of Rel B in transient transfections was performed. Two groups were analyzed in triplicate each. The First group was SKOVÂ· cells transfected with iRNARelB and the other group was transfected with siRNALuciferase.

2015-10-31 | E-GEOD-62815 | biostudies-arrayexpress

EZH2 promotes a bi-lineage identity in basal-like breast cancer cells

Project description:The mechanisms regulating breast cancer differentiation state are poorly understood. Of particular interest are molecular regulators controlling the highly aggressive and poorly differentiated traits of basal-like breast carcinomas. Here we show that the Polycomb factor EZH2 maintains the differentiation state of basal-like breast cancer cells, and promotes the expression of progenitor-associated and basal-lineage genes. Specifically, EZH2 regulates the composition of basal-like breast cancer cell populations by promoting a M-bM-^@M-^\bi-lineageM-bM-^@M-^] differentiation state, in which cells co-express basal- and luminal-lineage markers. We show that human basal-like breast cancers contain a subpopulation of bi-lineage cells, and that EZH2-deficient cells give rise to tumors with a decreased proportion of such cells. Bi-lineage cells express genes that are active in normal luminal progenitors, and possess increased colony formation capacity, consistent with a primitive differentiation state. We found that GATA3, a driver of luminal differentiation, performs a function opposite to EZH2, acting to suppress bi-lineage identity and luminal progenitor gene expression. GATA3 levels increase upon EZH2 silencing, leading to the observed decrease in bi-lineage cell numbers. Our findings reveal a novel role for EZH2 in controlling basal-like breast cancer differentiation state and intra-tumoral cell composition. Total of four treatments (HCC70 cells stably expressing shEZH2, shEED, or EZH2 cDNA, and MDA-MB-468 cells stably expressing shEZH2) were done in duplicates, each with its own control.

2012-09-21 | E-GEOD-36939 | biostudies-arrayexpress

Epigenetic silencing of Th1 chemokines shapes tumor immunity, immunotherapy and patient outcome [shEZH2]

2015-08-11 | GSE71870 | GEO

Epigenetic silencing of Th1 chemokines shapes tumor immunity, immunotherapy and patient outcome [GSK126]

2015-08-11 | GSE71869 | GEO

Gene expression profile of gastric cancer stem cells after CD44 knockdown

Project description:We did the microarray to further compare the changes of gene expression between gastric cancer stem cells with CD44 knockdown by lentivirus and gastric cancer stem cells by scamble short hairpin RNA. Gastric cancer stem cells (Lentivirus) were infected with lentivirus that expressed human CD44-speciï¬c short hairpin RNA (shRNA). Control group of gastric cancer stem cells (Vector group) were only infected with scramble shRNA.

2015-12-31 | E-GEOD-58143 | biostudies-arrayexpress

Epigenetic silencing of Th1 chemokines shapes tumor immunity, immunotherapy and patient outcome [shEZH2]

Project description:To define the gene profile altered by EZH2 and H3K27me3 in response to IFNg, we performed several microarrays in primary ovarian cancer cells transfected with shEZH2 or treated with GSK126. We found that 155 and 124 genes were altered by shEZH2 and GSK126 treatment, respectively, and 20 genes were increased or decreased by both shEZH2 and GSK126 treatment. Primary ovarian cancer cells were pretreated with GSK126, or transduced with a shEZH2 lentivirus, and stimulated with IFNg for 24 hours. RNA were isolated by Rneasy kit according to the manufacturer's protocol, and applied for affymetrix microarray at University of Michigan DNA Sequencing Core

2015-08-11 | E-GEOD-71870 | biostudies-arrayexpress

Epigenetic silencing of Th1 chemokines shapes tumor immunity, immunotherapy and patient outcome [GSK126]

2015-08-11 | E-GEOD-71869 | biostudies-arrayexpress

Differential gene expression profiles between SKOV3.ip1-S116A cells (Ser116 of PEA-15 substituted with alanine) and SKOV3.ip1-S116D cells (Ser116 of PEA-15 substituted with aspartic acid).

Project description:To dissect the molecular mechanisms of PEA-15-mediated paclitaxel sensitization in ovarian cancer cells, we performed cDNA microarray analysis using SKOV3.ip1-S116A cells (Ser116 of PEA-15 substituted with alanine) and SKOV3.ip1-S116D cells (Ser116 of PEA-15 substituted with aspartic acid). cDNA microarray data analysis showed that SCLIP (SCG10-like protein), also known as STMN3, was highly expressed in SKOV3.ip1-S116D cells and was involved in pPEA-15-mediated paclitaxel sensitization in ovarian cancer cells. SKOV3.ip1-S116A cells (Ser116 of PEA-15 substituted with alanine) and SKOV3.ip1-S116D cells (Ser116 of PEA-15 substituted with aspartic acid) were used. Total RNA was extracted and purified using RNeasy mini kit (Qiagen, Inc.) according to the manufacturerM-bM-^@M-^Ys instructions. The integrity of the obtained RNA was assessed using an Agilent 2100 BioAnalyzer (Agilent Technologies). The Affymetrix HGU133 plus platform was used for hybridization, staining, and imaging of the arrays by following the manufacturerM-bM-^@M-^Ys instructions. Gene expression analysis was performed in triplicate.

2012-05-11 | E-GEOD-37934 | biostudies-arrayexpress

The effect of EZH2 knockdown on gene expression in KDM6A-deficient KYSE180 cells following exposure to ionizing radiation [RNA-seq]

Project description:To elucidate the mechanism by which EZH2 regulates the radiosensitivity of KDM6A-deficient ESCC cells, we established KYSE180-shEZH2 and control KYSE180-shluc cells. 48 hours after exposure to 6Gy IR, we performed gene expression profiling analysis using RNA-seq data from KYSE180-shEZH2 and control KYSE180-shluc.

2024-04-22 | GSE264079 | GEO

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