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Sample GSM492517 Query DataSets for GSM492517
Status Public on Apr 19, 2010
Title Integrative genomics of ovarian cancer IC407 [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: 3
age: 83
scandate(batch): 10-31-07
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 1.3104900121689
CN_473964 1.6311800479889
CN_473965 2.1589999198914
CN_477984 2.0798699855804
CN_473981 0.95076501369476
CN_473982 1.7815899848938
CN_497980 1.9413100481033
CN_497981 2.185359954834
CN_513369 3.4239799976349
CN_513370 1.6726800203323
CN_517762 1.4026299715042
CN_517763 2.6030099391937
CN_502615 2.830549955368
CN_502613 1.9519599676132
CN_502614 3.3660399913788
CN_502616 1.2853000164032
CN_502842 2.7152099609375
CN_502843 1.3798799514771
CN_466171 1.6986900568008
CN_466172 1.9527900218964

Total number of rows: 1870003

Table truncated, full table size 51343 Kbytes.

Supplementary file Size Download File type/resource
GSM492517_IC407N.CEL.gz 32.2 Mb (ftp)(http) CEL
GSM492517_IC407T.CEL.gz 32.3 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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