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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Copy number analysis of spontaneously transformed hTERT-immortalized ovarian surface epithelial cells

ABSTRACT: We present evidence for cytogenetic changes in two transformed ovarian surface epithelium cell lines, TOSE1 and TOSE4. hTERT-immortalised ovarian surface epithelial cell line spontaneously transformed as measured by growth in soft agar. These cells were grown on plastic, and genomic DNA was extracted and analyzed for cytogenetic changes. The genotyping Affymetrix SNP6.0 arrays were used to define copy number changes in the TOSE1 and TOSE4 cell lines.

ORGANISM(S): Homo sapiens

SUBMITTER: Hagen Kulbe

PROVIDER: E-GEOD-25492 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Copy number analysis of spontaneously transformed hTERT-immortalized ovarian surface epithelial cells

Project description:We present evidence for cytogenetic changes in two transformed ovarian surface epithelium cell lines, TOSE1 and TOSE4. hTERT-immortalised ovarian surface epithelial cell line spontaneously transformed as measured by growth in soft agar. These cells were grown on plastic, and genomic DNA was extracted and analyzed for cytogenetic changes.

2010-11-19 | GSE25492 | GEO

Cyto2.7M copy number analysis of eight diffuse large B-cell samples and one matched blood sample

Project description:We performed a comparison analysis of the Affymetrix arrays SNP6.0 genome wide array (SNP6.0) and cytogenetic 2.7M whole-genome array (Cyto2.7M) using nine human samples. We compared the two array types with respect to four parameters including the size and breakpoints of the alterations detected, the actual CN assigned to the CNVs as well as long stretches of loss of heterozygosity. Overall, we found very good consistency between the two types of array on all parameters compared, even in regions with very complex changes. This GEO submission contains the Cyto2.7M data. GEO submission, GSE37977 contains the SNP6.0 data.

2012-11-26 | GSE37978 | GEO

SNP6.0 copy number analysis of eight diffuse large B-cell samples and one matched blood sample

Project description:We performed a comparison analysis of the Affymetrix arrays SNP6.0 genome wide array (SNP6.0) and cytogenetic 2.7M whole-genome array (Cyto2.7M) using nine human samples. We compared the two array types with respect to four parameters including the size and breakpoints of the alterations detected, the actual CN assigned to the CNVs as well as long stretches of loss of heterozygosity. Overall, we found very good consistency between the two types of array on all parameters compared, even in regions with very complex changes. This GEO submission contains the SNP6.0 data. GEO submission, GSE37978 contains the Cyto2.7M data.

2012-11-26 | GSE37977 | GEO

Performance Comparison of the Affymetrix SNP6.0 and Cytogenetic 2.7M Whole-genome Microarrays in Complex Cancer Samples

Project description:We performed a comparison analysis of the Affymetrix arrays SNP6.0 genome wide array (SNP6.0) and cytogenetic 2.7M whole-genome array (Cyto2.7M) using nine human samples. We compared the two array types with respect to four parameters including the size and breakpoints of the alterations detected, the actual CN assigned to the CNVs as well as long stretches of loss of heterozygosity. Overall, we found very good consistency between the two types of array on all parameters compared, even in regions with very complex changes. This SuperSeries is composed of the SubSeries listed below.

2012-11-26 | GSE37979 | GEO

Integrative genomics identifies molecular alterations that differentiate superficial spreading and nodular melanoma

Project description:This SuperSeries is composed of the following subset Series: GSE22301: Gene expression data from melanoma cell lines and melanocyte controls GSE22305: Affymetrix SNP6.0 Array data for melanoma cell lines Refer to individual Series

2010-12-01 | E-GEOD-22306 | biostudies-arrayexpress

Expression data from M0505 and STOSE murine ovarian surface epithelial cell lines

Project description:Our lab established the M0505 cell line from the ovarian surface epithelium (OSE) of FVB/N mice in May 2005 in order to study OSE biology. This cell line spontaneously transformed into the spontaneously transformed OSE (STOSE) cell line in mid 2012. We used microarrays to try to determine the molecular pathways that may have lead to the transformation of M0505 cells into STOSE cells to gain information that may lead to a greater understanding of human ovarian cancer initiation.

2014-02-04 | GSE54633 | GEO

Expression data from M0505 and STOSE murine ovarian surface epithelial cell lines

2014-02-04 | E-GEOD-54633 | biostudies-arrayexpress

miRNAs in ovarian cancer: A systems approach (miRNA data)

Project description:MicroRNAs (miRNAs) are short (~22 nucleotides) regulatory RNAs that can modulate gene expression and are aberrantly expressed in many diseases including cancer. We report the results of a systems analysis of miRNA regulation in ovarian cancer. We found that 33 miRNAs are up-regulated and 9 down-regulated in CEPI relative to OSE (p<0.01, ≥2 fold change). Of these, 12 were previously annotated miRNAs (Sanger miRBase) of which 9 are up-regulated and 3 are down-regulated in CEPI relative to OSE. Current models predict that changes in levels of miRNAs will be inversely correlated with changes in the levels of targeted mRNAs due to miRNA regulation. This predicted inverse correlation held for only ~9% of predicted target mRNAs. Computational analyses indicate the unexpected low inverse correlation may be at least partially explained by variation in the number of miRNA binding sites within the 3’ UTRs of targeted mRNAs and by miRNA-mediated changes in levels of transcription factors that can exert overriding trans-regulatory controls on target loci. miRNAs were collected from three laser captured microdissected ovarian cancer epithelial (CEPI) samples. The miRNA expression pattern was compared with three healthy ovarian surface epithelia samples as controls using a custom-manufactured Affymetrix GeneChip® array.

2011-07-28 | E-GEOD-23383 | biostudies-arrayexpress

Homo sapiens

Project description:Copy number analysis of spontaneously transformed hTERT-immortalized ovarian surface epithelial cells

| PRJNA134625 | ENA

GeneChip Mapping 500K set and Genome-Wide Human SNP 6.0 Array in meningioma tumors

Project description:Cytogenetic profiles of 50 meningiomas using high-density GeneChip Mapping 500K set and Genome-Wide Human SNP 6.0 Array in the tumor tissues and in the peripheral blood of the same patients. A total of two hundred 500k arrays (100 tumor samples and 100 blood samples) and 14 SNP6.0 arrays (7 tumour samples and 7 peripheral blood samples) were studied to explore the most common recurrent chromosomal abnormalities (gains and losses) in meningiomas. Our results confirm that del(22q) (52%) and del(1p) (16%) (common deleted regions: 22q11.21-22q13.3. and 1p31.2-p36.33) are the most frequent abnormalities. Additionally, recurrent monosomy 14 (8%), del(6p) (10%), del(7p) (10%) and del(19p) (6%) were also observed, while copy number variation (CNV) patterns consistent with recurrent chromosome gains, gene amplification was absent or rare. Based on their overall SNP profiles meningiomas could be classified into: i) diploid cases, ii) meningiomas with a single chromosome change (e.g. monosomy 22/del(22q) and iii) tumours with M-bM-^IM-%2 altered chromosomes. 500K SNP mapping set array and Genome-Wide Human SNP 6.0 Array were used to profile 50 meningiomas with matched blood DNA samples. Loss of heterozygosity (LOH) and copy number abnormality (CNA) profiles were derived from each tumour-blood pair. In seven tumors, both types of arrays were assessed.

2012-11-30 | E-GEOD-42624 | biostudies-arrayexpress

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