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Series GSE146554 Query DataSets for GSE146554
Status Public on Mar 06, 2020
Title Global DNA hypomethylation in ovarian cancer (CNV_data)
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary Comparison of DNA methylome, mRNA transcriptome, and copy number variation in tumors with global loss of DNA methylation to tumors with normal global methylation.
 
Overall design Human tissue samples were obtained from patients undergoing surgical resection at Roswell Park Comprehensive Cancer Center, using Institutional Review Board Protocol I-215512. Normal controls were obtained from patients without malignancy, and tumor samples contained >90% neoplastic cells. IOSE-121 and OVCAR3 cells at ~50% confluence were treated with decitabine or PBS vehicle control. Affymetrix HG 1.0ST arrays and Total RNA-sequencing were used to analyze gene expression. Total RNA sequencing used the Illumina TruSeq Stranded Total RNA kit and an Illumina HiSeq 2000 Genome Analyzer. Illumina Infinium 450K BeadChips and Agilent SureSelect Methylome sequencing were used to analyze DNA methylation. High-throughput sequencing of library tags was performed using an Illumina HiSeq 2000 Genome Analyzer. Genomic copy number analysis was performed using Affymetrix Cytoscan HD microarrays.
 
Contributor(s) Karpf AR, Albahrani M
Citation(s) 32213861
Submission date Mar 06, 2020
Last update date Apr 20, 2020
Contact name Adam R Karpf
E-mail(s) adam.karpf@unmc.edu
Phone 402-559-6115
Organization name UNMC
Street address S 42nd &, Emile St
City Omaha
State/province NE
ZIP/Postal code 68198
Country USA
 
Platforms (1)
GPL16131 [CytoScanHD_Array] Affymetrix CytoScan HD Array
Samples (40)
GSM4392205 EOC61: Female high grade serous ovarian cancer, primary tumor
GSM4392206 EOC74: Female high grade serous ovarian cancer, primary tumor
GSM4392207 EOC82: Female high grade serous ovarian cancer, primary tumor
This SubSeries is part of SuperSeries:
GSE146556 Global DNA hypomethylation in ovarian cancer
Relations
BioProject PRJNA610852

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE146554_RAW.tar 1.1 Gb (http)(custom) TAR (of CEL, TXT)
Processed data provided as supplementary file

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