|
| Status |
Public on May 13, 2015 |
| Title |
Tumor DNA |
| Sample type |
genomic |
| |
|
| Source name |
Pheochromocytoma
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: male pheochromocytoma tissue
tissue: pheochromocytoma tissue
|
| Treatment protocol |
not applicable
|
| Growth protocol |
not applicable
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated using a Gentrakit according manufacturers procedures
|
| Label |
Cy3 and Cy5
|
| Label protocol |
According standard Illumina procedures
|
| |
|
| Hybridization protocol |
According standard Illumina procedures
|
| Scan protocol |
As described by S. Hopman et al, Eur J Cancer 2013
|
| Description |
snap frozen pheochromocytoma tissue
|
| Data processing |
Data for each bead chip were self-normalized in Genomestudio GT (Illumina) using information contained within the array. Copy number estimates for each individual sample were determined by comparison with a common reference set of 200 samples from the HapMAP project (www.hapmap.org/downloads/raw_data) supplied by Illumina (Manifest files) and visualized in the Nexus software program (version five, Biodiscovery, El Segundo, CA, USA) as log2 ratios.
Nexus normalized log R intensities and B-allele frequencies
|
| |
|
| Submission date |
May 12, 2015 |
| Last update date |
May 13, 2015 |
| Contact name |
Esther Korpershoek |
| E-mail(s) |
e.korpershoek.1@erasmusmc.nl
|
| Organization name |
Erasmus MC University Medical Center Rotterdam
|
| Department |
Pathology
|
| Street address |
Wytemaweg 80
|
| City |
Rotterdam |
| ZIP/Postal code |
3015CN |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL13135 |
| Series (1) |
| GSE68794 |
A large germline alteration affecting MAX and FUT8, causing familial bilateral malignant pheochromocytoma and renal oncocytoma |
|
