GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM492562 Query DataSets for GSM492562
Status Public on Apr 19, 2010
Title Integrative genomics of ovarian cancer P4219 [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: 3c
age: -
scandate(batch): 4-16-08
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 3.2572200298309
CN_473964 1.6082899570465
CN_473965 2.4142999649048
CN_477984 1.3231500387192
CN_473981 2.2812900543213
CN_473982 1.4280200004578
CN_497980 3.4114799499512
CN_497981 1.774719953537
CN_513369 4.4431099891663
CN_513370 1.787260055542
CN_517762 1.2821500301361
CN_517763 0.98318099975586
CN_502615 3.5913200378418
CN_502613 1.9435299634933
CN_502614 3.8409600257874
CN_502616 4.4967699050903
CN_502842 1.6181700229645
CN_502843 2.2283799648285
CN_466171 1.9921900033951
CN_466172 1.5605900287628

Total number of rows: 1870003

Table truncated, full table size 51429 Kbytes.

Supplementary file Size Download File type/resource
GSM492562_P4219N.CEL.gz 28.1 Mb (ftp)(http) CEL
GSM492562_P4219T.CEL.gz 29.3 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap