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Sample GSM492565 Query DataSets for GSM492565
Status Public on Apr 19, 2010
Title Integrative genomics of ovarian cancer P5390 [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
histological subtype: clear cell
grade: 3
stage: 3c
age: -
scandate(batch): 6-24-08
source: Tissue_bank
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
E-mail(s) manasa.ramakrishna@petermac.org
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
ID_REF
VALUE ratio

Data table
ID_REF VALUE
CN_473963 8.1521902084351
CN_473964 4.9816999435425
CN_473965 3.7427499294281
CN_477984 2.9329600334167
CN_473981 5.3167099952698
CN_473982 2.9959099292755
CN_497980 3.180860042572
CN_497981 2.8647799491882
CN_513369 7.7634000778198
CN_513370 2.7358100414276
CN_517762 6.4506301879883
CN_517763 2.2121000289917
CN_502615 5.5329599380493
CN_502613 2.2654299736023
CN_502614 4.3581500053406
CN_502616 9.5895595550537
CN_502842 3.1913800239563
CN_502843 3.6954998970032
CN_466171 2.3946299552917
CN_466172 2.4342000484467

Total number of rows: 1870003

Table truncated, full table size 51295 Kbytes.




Supplementary file Size Download File type/resource
GSM492565_P5390T.CEL.gz 30.3 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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