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Transcription profiling of 285 human ovarian tumour samples

ABSTRACT: We used microarrays to profile the expression levels of 285 ovarian samples in order to identify molecular subtypes of the tumour Experiment Overall Design: Randomly selected samples from the AOCS ( Australian Ovarian Cancer Study) was expression profiled on the affymetrix U133_plus2 platform to identify novel subtypes of ovarian tumour

ORGANISM(S): Homo sapiens

SUBMITTER: Prof David Bowtell PhD

PROVIDER: E-GEOD-9891 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression profile of 285 ovarian tumour samples

Project description:We used microarrays to profile the expression levels of 285 ovarian samples in order to identify molecular subtypes of the tumour Keywords: disease state analysis

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Transcription profiling of human ovarian tumour samples

Project description:This SuperSeries is composed of the following subset Series:; GSE9890: Expression profile of 5 ovarian tumour samples (two different cell types from each sample profiles); GSE9891: Expression profile of 285 ovarian tumour samples Experiment Overall Design: Refer to individual Series

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Project description:Investigation of malignancy-associated expression of gene sets based on ovarian tumour histone modification status. A single serous epithelial ovarian tumour (which was assayed using ChIP-seq to determine histone modification profiles; SRA059358) was profiled using the HGU133 plus 2 GeneChip, along with 8 benign ovarian lesions (1 serous cyst, 3 serous cystadenomas and 4 serous cystadenofibromas) for comparison. Expression levels of genes marked in the tumour with particular histone modifications were compared between the tumour and the benign samples.

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Profiling of ovarian tumour and benign lesions

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17β-estradiol accelerates ovarian tumour progression in vivo though the upregulation of GREB1

Project description:Exogenous 17β-estradiol (E2) accelerates the progression of ovarian cancer in the transgenic tgCAG-LS-TAg mouse model of the disease. We hypothesized that E2 has direct effects on ovarian cancer cells and this study was designed to determine the molecular mechanisms by which E2 accelerates ovarian tumour progression. Mouse ovarian cancer ascites (MASE2) cell lines were derived from tgCAG-LS-TAg mice. Following intraperitoneal engraftment of MASE2 into SCID mice, exogenous E2 significantly decreased the survival time and increased the tumour burden. Microarray analysis performed on cells derived from mouse ovarian cancer ascites (MASE2) treated with and without E2 indicated that E2 treatment caused the upregulation and downregulation of genes involved in cell differentiation, proliferation and migration. In particular, Greb1 that has been also identified as a hormone-responsive gene in breast cances, was upregulated in mouse tumour cells treated with E2. Three biological replicates (MASE2 tumours grown in SCID mice, see growth protocol) were analyzed for both conditions of addition of E2 or placebo.

2014-01-20 | E-GEOD-45271 | biostudies-arrayexpress

Chromatin H3K27me3/H3K4me3 histone marks define gene sets in high grade serous ovarian cancer that distinguish malignant, tumour sustaining and chemo-resistant ovarian tumour cells.

Project description:This SuperSeries is composed of the following subset Series: GSE41498: Profiling of ovarian tumour and benign lesions GSE41499: Expression profiling of ovarian cancer cell lines Refer to individual Series

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17β-estradiol accelerates ovarian tumour progression in vivo though the upregulation of GREB1

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Transcription profiling of repeatedly thaw-frozen ovarian tumour samples

Project description:We evaluated the influence of repeatedly division of tumour samples at room temperature on gene expression profile. Experimental Design: four old (more than five years) ovarian tumour samples were divided twice on two different days giving a total of three aliquots each. RNA from the removed tissue aliquot was extracted and purified at the day of division and the remaining tissue re-frozen. The Trizol reagent kit and RNeasy MinElute kit were used for RNA extraction and purification. RNA quantity was evaluated on a spectrophotometer and quality was evaluated on the Agilent Bioanalyzer 2100. RNA from all three aliquots of the four old tumour samples were labeled with the ENZO kit and hybridized to twelve Affymetrix chips U133A 2.0. The four tumours were named 2, 3, 4 and 7. Aliquots from the first day are called "a", from the second day "b", the third day "c".

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Homo sapiens

Project description:Expression profile of 285 ovarian tumour samples

| PRJNA105139 | ENA

Characterization of novel ovarian tumor cell lines that retain the phenotype of primary tumors [Illumina]

Project description:The inability to establish stable cell lines from the vast majority of human tumors has limited the use of in vitro models to study human cancer. Currently available tumor cell lines fail to represent the biological diversity of human tumors. We have developed a cell culture medium that enabled us to routinely establish cell lines from diverse subtypes of ovarian tumors. Importantly, the twenty-five ovarian tumor cell lines described here retain the genomic landscape, histopathology, and molecular features of the original tumors. Furthermore, the molecular profile and drug response of these cell lines correlated with distinct groups of primary tumors with different outcomes. Thus, tumor cell lines derived using this methodology represent a significantly improved new platform to study human tumor biology and treatment. Total RNA was obtained from untreated ovarian cancer cell lines and clustering analysis was performed. The 'Median-Cent_5147_probes.txt' is a list of the 5147 gene probes that has at least 2-fold difference relative to median value across cell lines in at least 4 samples. These are the probes that were used for hierarchial clustering analysis. The 'Combined_and_GSE9891.txt' is a combination of gene probes from this study of ovarian cell lines and of human ovarian cancer cell lines (GSE9891[GPL570]: Expression profile of 285 ovarian tumour samples). Only the 3832 overlapping gene probes between the this study and the GSE9891[GPL570] study are listed. The 3832 gene probes listed have at least 2-fold difference relative to median value across samples in at least 4 samples.

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