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Sample GSM492510 Query DataSets for GSM492510
Status Public on Apr 19, 2010
Title Integrative genomics of ovarian cancer IC315 [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: -
age: 82
scandate(batch): 1-10-08
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 3.6838300228119
CN_473964 3.2609798908234
CN_473965 3.0401799678802
CN_477984 1.9460200071335
CN_473981 2.0477600097656
CN_473982 2.7288401126862
CN_497980 1.856299996376
CN_497981 4.209939956665
CN_513369 1.5939300060272
CN_513370 2.3031799793243
CN_517762 1.7810499668121
CN_517763 2.4934000968933
CN_502615 2.6008899211884
CN_502613 1.5192799568176
CN_502614 2.0023000240326
CN_502616 2.4558000564575
CN_502842 2.9939699172974
CN_502843 3.2493801116943
CN_466171 4.3772501945496
CN_466172 1.648609995842

Total number of rows: 1870003

Table truncated, full table size 51305 Kbytes.

Supplementary file Size Download File type/resource
GSM492510_IC315N.CEL.gz 32.3 Mb (ftp)(http) CEL
GSM492510_IC315T.CEL.gz 31.8 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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