|
| Status |
Public on Apr 19, 2010 |
| Title |
Integrative genomics of ovarian cancer IC258 [HuGene-1_0-st] |
| Sample type |
RNA |
| |
|
| Source name |
Ovarian tumours at the time of diagnosis
|
| Organism |
Homo sapiens |
| Characteristics |
histological subtype: endometrioid
grade: 3
stage: 3
age: 69
batch: 5
|
| Treatment protocol |
All tumours were fresh-frozen and OCT embedded. Lymphocytic DNA was extracted from stored blood samples.
|
| Extracted molecule |
total RNA |
| 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 |
Gene Expression Data from Epithelial ovarian cancers
|
| Data processing |
QC measures using Affymetrix Genotyping Conole and “affyPLM” package in the R open-source environment. Arrays were normalised using robust multichip average (rma) in the aroma.affymetrix package. All gene expression analyses were performed in the R environment using limma package.
|
| |
|
| Submission date |
Dec 17, 2009 |
| Last update date |
Apr 19, 2010 |
| 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 |
GPL6244 |
| Series (1) |
| GSE19539 |
Identification of Novel Oncogene Loci in Ovarian Cancer through Integrated Copy Number and Expression Analysis |
|
