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Sample GSM492506 Query DataSets for GSM492506
Status Public on Apr 19, 2010
Title Integrative genomics of ovarian cancer IC258 [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: endometrioid
grade: 3
stage: 3c
age: 69
scandate(batch): 1-10-08
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 2.3683300018311
CN_473964 1.9957100152969
CN_473965 1.5952399969101
CN_477984 1.6089999675751
CN_473981 1.8490699529648
CN_473982 2.3571200370789
CN_497980 2.1671199798584
CN_497981 2.9971499443054
CN_513369 2.7074799537659
CN_513370 2.4839301109314
CN_517762 1.4536000490189
CN_517763 2.415549993515
CN_502615 1.3068799972534
CN_502613 2.2312200069427
CN_502614 1.3550000190735
CN_502616 2.0891199111938
CN_502842 1.6816300153732
CN_502843 1.4891300201416
CN_466171 2.8609299659729
CN_466172 1.1388399600983

Total number of rows: 1870003

Table truncated, full table size 51304 Kbytes.

Supplementary file Size Download File type/resource
GSM492506_IC258N.CEL.gz 32.5 Mb (ftp)(http) CEL
GSM492506_IC258T.CEL.gz 33.1 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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