Global DNA hypomethylation in ovarian cancer (CNV_data)

Comparison of DNA methylome, mRNA transcriptome, and copy number variation in tumors with global loss of DNA methylation to tumors with normal global methylation. 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.