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Sample GSM492561 Query DataSets for GSM492561
Status Public on Apr 19, 2010
Title Integrative genomics of ovarian cancer P4178 [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: 3
stage: 3
age: -
scandate(batch): 10-24-08
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 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 1.5907299518585
CN_473964 1.2154200077057
CN_473965 1.2619400024414
CN_477984 0.99698799848557
CN_473981 1.7469600439072
CN_473982 1.7923599481583
CN_497980 1.1684000492096
CN_497981 2.2439000606537
CN_513369 2.8126699924469
CN_513370 2.1302800178528
CN_517762 1.1388200521469
CN_517763 1.4449599981308
CN_502615 4.4194102287292
CN_502613 1.5694899559021
CN_502614 1.0533100366592
CN_502616 1.2600100040436
CN_502842 1.9580700397491
CN_502843 1.2398099899292
CN_466171 1.1029399633408
CN_466172 1.578430056572

Total number of rows: 1870003

Table truncated, full table size 51340 Kbytes.

Supplementary file Size Download File type/resource
GSM492561_P4178N.CEL.gz 27.7 Mb (ftp)(http) CEL
GSM492561_P4178T.CEL.gz 28.7 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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