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Sample GSM492514 Query DataSets for GSM492514
Status Public on Apr 19, 2010
Title Integrative genomics of ovarian cancer IC328 [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: serous
grade: 2
stage: -
age: 66
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 Jul 09, 2014
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
Affiliated with GSE58579

Data table header descriptions
VALUE ratio

Data table
CN_473963 2.5744800567627
CN_473964 1.7221599817276
CN_473965 2.1236600875854
CN_477984 1.4599299430847
CN_473981 4.4873099327087
CN_473982 3.4095098972321
CN_497980 2.3495199680328
CN_497981 4.131420135498
CN_513369 2.685329914093
CN_513370 2.3232700824738
CN_517762 1.5237200260162
CN_517763 1.4707200527191
CN_502615 1.0290299654007
CN_502613 2.8488800525665
CN_502614 2.3367900848389
CN_502616 3.5804300308228
CN_502842 1.3557200431824
CN_502843 1.5154099464417
CN_466171 2.0719599723816
CN_466172 1.2310800552368

Total number of rows: 1870003

Table truncated, full table size 51330 Kbytes.

Supplementary file Size Download File type/resource
GSM492514_IC328N.CEL.gz 29.8 Mb (ftp)(http) CEL
GSM492514_IC328T.CEL.gz 32.0 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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