|
| 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 |
| E-mail(s) |
manasa.ramakrishna@petermac.org
|
| 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 |
|
| Relations |
| Affiliated with |
GSE58579 |
