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Sample GSM492505 Query DataSets for GSM492505
Status Public on Apr 19, 2010
Title Integrative genomics of ovarian cancer IC257 [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: mucinous
grade: 1
stage: 1a
age: 60
scandate(batch): 2-26-08
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 1.4583300352097
CN_473964 1.6281000375748
CN_473965 1.543319940567
CN_477984 2.2617700099945
CN_473981 1.1894600391388
CN_473982 2.4955899715424
CN_497980 1.7312200069427
CN_497981 1.3867599964142
CN_513369 1.4078999757767
CN_513370 1.7943999767303
CN_517762 2.1159000396729
CN_517763 2.1548700332642
CN_502615 1.2205499410629
CN_502613 1.2287800312042
CN_502614 1.7697199583054
CN_502616 2.5352499485016
CN_502842 1.9172500371933
CN_502843 2.0365200042725
CN_466171 1.4749300479889
CN_466172 1.5975799560547

Total number of rows: 1870003

Table truncated, full table size 51278 Kbytes.

Supplementary file Size Download File type/resource
GSM492505_IC257N.CEL.gz 31.8 Mb (ftp)(http) CEL
GSM492505_IC257T.CEL.gz 31.2 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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