|
| Status |
Public on Jun 28, 2010 |
| Title |
Ovarian cancer cell line PEO1 |
| Sample type |
genomic |
| |
|
| Source name |
Ovarian cancer cell line PEO1
|
| Organism |
Homo sapiens |
| Characteristics |
patient number: 2
disease stage: Post-treatment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.
|
| Label |
C-Bio and A-DNP
|
| Label protocol |
750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).
|
| |
|
| Hybridization protocol |
RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).
|
| Scan protocol |
After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).
|
| Description |
Genomic DNA extracted from PEO1 was genotyped using Illumina Infinium Human1M-Duo Genotyping BeadChips (Illumina).
|
| Data processing |
Data was processed in BeadStudio using the standard Illumina protocol. Log R Ratio and B Allele Frequency values were produced by tQN (Staaf et al 2008)
|
| |
|
| Submission date |
Oct 07, 2009 |
| Last update date |
May 18, 2011 |
| Contact name |
Charlotte K Y Ng |
| Organization name |
University Hospital Basel
|
| Department |
Pathology
|
| Street address |
Schönbeinstrasse 40
|
| City |
Basel |
| ZIP/Postal code |
4003 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL6984 |
| Series (1) |
| GSE18461 |
Copy number profiling of PE ovarian cancer lines |
|
