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Sample GSM492519 Query DataSets for GSM492519
Status Public on Apr 19, 2010
Title Integrative genomics of ovarian cancer IC419 [GenomeWideSNP_6]
Sample type genomic
Source name Ovarian tumours at the time of diagnosis
Organism Homo sapiens
Characteristics tissue type (t=tumour; n= normal blood lymphocyte): T&N
histological subtype: clear cell
grade: 2
stage: 1
age: 65
scandate(batch): 6-24-08
source: Campbell
Treatment protocol All tumours were fresh-frozen and OCT embedded. Lymphocytic DNA was extracted from stored blood samples.
Extracted molecule genomic DNA
Extraction protocol 10uM slices of tumour were hand-microdissected to obtain regions with >80% epithelial cells and reduce contamination from fibroblasts, blood vessels etc. Following this, for DNA extraction, slides containing sections were stained with Haematoxylin and Eosin and DNA was extracted using the Qiagen DNEasy kit. For RNA, identical slides were stained with Cresyl violet and total RNA was extracted using the Ambion mirVana kit according to manufacturer's instructions.
Label biotin
Label protocol According to Affymetrix protocol, Biotin labelled
Hybridization protocol According to Affymetrix protocol using recommended instrumentation
Scan protocol According to Affymetrix protocol and using GeneChip Operating Software
Description none
Data processing primary data description: Partek's copy number workflow generates copy number ratios relative to matching normal samples or a pooled baseline and then converts and presents these values as whole copy numbers. The file titled SNP6_Normalised-Copy-number.csv contains these values for each sample. In this file, probes on Chromosome Y and the Mitochondrion (MT) have been removed and the probesets are organised first by Chromosome and then by start position. Annotations for this were mapped in Partek using the Affymetrix GenomewideSNP6, CN and SNP annotation files, release number 23. This data was then used for Segmentation using the CBS algorithm in the DNAcopy package in R open-source software.
Submission date Dec 31, 2009
Last update date Apr 19, 2010
Contact name Manasa Ramakrishna
Organization name Peter MacCallum Cancer Centre
Street address St Andrew's Pl
City Melbourne
State/province Victoria
ZIP/Postal code 3002
Country Australia
Platform ID GPL6801
Series (1)
GSE19539 Identification of Novel Oncogene Loci in Ovarian Cancer through Integrated Copy Number and Expression Analysis

Data table header descriptions
VALUE ratio

Data table
CN_473963 2.0271899700165
CN_473964 1.3627400398254
CN_473965 1.6963200569153
CN_477984 2.3887600898743
CN_473981 3.0622398853302
CN_473982 3.1012499332428
CN_497980 2.0206398963928
CN_497981 1.9658600091934
CN_513369 2.7333600521088
CN_513370 2.0915598869324
CN_517762 1.6308799982071
CN_517763 1.6964900493622
CN_502615 1.3666299581528
CN_502613 1.2413599491119
CN_502614 2.8171100616455
CN_502616 2.3163299560547
CN_502842 3.2579300403595
CN_502843 1.4665900468826
CN_466171 1.1525700092316
CN_466172 2.3060700893402

Total number of rows: 1870003

Table truncated, full table size 51281 Kbytes.

Supplementary file Size Download File type/resource
GSM492519_IC419N.CEL.gz 30.6 Mb (ftp)(http) CEL
GSM492519_IC419T.CEL.gz 31.6 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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