|
| Status |
Public on Feb 26, 2010 |
| Title |
case 1 genotype |
| Sample type |
genomic |
| |
|
| Source name |
GCT patient case
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary intracranial pediatric germ cell tumor (GCT)
diagnosis: germinoma
age: 13.6 years
|
| 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 |
200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C 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 48ºC, 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 germ cell tumors was genotyped using Infinium Human610_Quad Genotyping BeadChips (Illumina).
|
| Data processing |
Genomic DNA extracted from breast tumors was genotyped using Infinium Human610_Quad Genotyping BeadChips (Illumina).
|
| |
|
| Submission date |
Dec 09, 2009 |
| Last update date |
Feb 26, 2010 |
| Contact name |
Yu Hsuan Wu |
| E-mail(s) |
allenwu03@gmail.com
|
| Organization name |
National Yang-Ming University
|
| Street address |
No.155, Sec.2, Linong Street
|
| City |
Taipei |
| ZIP/Postal code |
112 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL8887 |
| Series (2) |
| GSE19349 |
Genotyping and analysis of chromosome copy number variation (CNV) from pediatric primary intracranial germ cell tumor |
| GSE19350 |
Array-based bioinformatic analysis on pediatric primary central nervous system germ cell tumors |
|
