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Sample GSM2723567 Query DataSets for GSM2723567
Status Public on Aug 01, 2017
Title HGSC_JB4853
Sample type genomic
 
Source name primary ovarian tumor tissue
Organism Homo sapiens
Characteristics stic: Yes
age: 65
path.stage: IIC
surgical.outcome: Optimal
diagnosis.of.record: Ovarian Ca
diagnosis.after.path.re.review: Fallopian Tube Ca
platinumfreeinterval.mos..: 44.1
platinumstatus: Sensitive
recurrence: N
pfs.mos..: 49
os.mos..: 49
vitalstatus: Alive
race: WHITE
tcga_subtype_dif: 0.036
tcga_subtype_imr: 0.516
tcga_subtype_mes: -0.354
tcga_subtype_pro: -0.145
tissue: primary tumor tissue from high grade serous ovarian tumors
Extracted molecule genomic DNA
Extraction protocol DNA and RNA were co-isolated from frozen tissue tumor blocks, and RNA was isolated from normal tissues utilizing Ambion’s ToTALLY RNA™ RNA Isolation Kit (Part Number AM1910, ©Ambion, Inc.). DNA concentration was confirmed using a PicoGreen protocol. RNA quality was confirmed by utilizing an Agilent Bioanalyzer and assigning an RNA Integrity Number (RIN) to each sample.
Label NA
Label protocol Total genomic DNA (500 ng) was collected from all 96 samples included in the study, and digested with Nsp I and Sty I restriction enzymes and ligated to adaptors.
 
Hybridization protocol The amplified DNA is then fragmented, labeled, and hybridized to a SNP Array 6.0 containing more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation.
Scan protocol All 96 samples were assayed at once, in a single batch
Data processing The Affy Power Tools (APT) copy number workflow was used to preprocess the SNP arrays and derive log R ratios representing relative copy number abundance. A standard HapMap reference included in the APT toolbox was used to represent a diploid genome. Circular binary segmentation (CBS) as implemented in the DNAcopy (Seshan VE and Olshen A. DNAcopy: DNA copy number data analysis. R package version 1.42.0) package from Bioconductor, using standard settings
The GISTIC2.0 algorithm was applied to the segmented data via the Genome Pattern online tool suite, using default settings, to make gene level copy number calls and identify significantly, copy number altered regions
 
Submission date Jul 31, 2017
Last update date Jan 23, 2018
Contact name leslie cope
E-mail(s) cope@jhu.edu
Organization name leslie cope
Street address 550 N. Broadway
City Baltimore
State/province MD
ZIP/Postal code 21209
Country USA
 
Platform ID GPL6801
Series (2)
GSE102085 Molecular analysis of high-grade serous ovarian carcinoma with and without associated serous tubal intra-epithelial carcinoma [CNV]
GSE102094 Molecular analysis of high-grade serous ovarian carcinoma with and without associated serous tubal intra-epithelial carcinoma

Supplementary file Size Download File type/resource
GSM2723567_04396_68_JB4853_GenomeWideSNP_6.CEL.gz 27.0 Mb (ftp)(http) CEL
Processed data are available on Series record

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