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Sample GSM492500 Query DataSets for GSM492500
Status Public on Apr 19, 2010
Title Integrative genomics of ovarian cancer IC138 [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: 47
scandate(batch): 4-16-08
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 2.743469953537
CN_473964 2.0791199207306
CN_473965 1.7983200550079
CN_477984 2.4853699207306
CN_473981 1.598799943924
CN_473982 2.3004200458527
CN_497980 1.925400018692
CN_497981 1.646399974823
CN_513369 3.0253300666809
CN_513370 1.5246599912643
CN_517762 3.1468799114227
CN_517763 1.614560008049
CN_502615 4.9123902320862
CN_502613 1.8320399522781
CN_502614 1.5350699424744
CN_502616 3.0506598949432
CN_502842 2.4698901176453
CN_502843 1.7700899839401
CN_466171 1.8304500579834
CN_466172 1.6053400039673

Total number of rows: 1870003

Table truncated, full table size 51321 Kbytes.

Supplementary file Size Download File type/resource
GSM492500_IC138N.CEL.gz 29.5 Mb (ftp)(http) CEL
GSM492500_IC138T.CEL.gz 29.2 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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