|
| Status |
Public on Jun 12, 2015 |
| Title |
Embryonal rhabdomyosarcoma in a Costello syndrome patient |
| Sample type |
genomic |
| |
|
| Source name |
Embryonal rhabdomyosarcoma in a Costello syndrome patient
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: tumor
disease state: Embryonal rhabdomyosarcoma in a Costello syndrome patient
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from a fresh-frozen tumor sample using the Quiagen Gentra Puregene Kit, as recommended by the Affymetrix CytoScan Assay user manual. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.
|
| Label |
biotin
|
| Label protocol |
As per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to the array (Affymetrix GeneChip Hybridization Oven 645) according to the manufacturer's instructions.
|
| Scan protocol |
The array was then washed using Affymetrix GeneChip fluidics station 450, and scanned using the Affymetrix GeneChip Scanner 3000.
|
| Data processing |
The array image was acquired using Affymetrix GeneChip Command Console Software. For confirmation, two Cytoscan HD arrays were performed for the tumor which gave similar results. Their raw DAT files were aligned and averaged by a proprietary C++ program (Microsoft, USA) for further analysis. CEL and CYCHP files were generated from the averaged DAT file using Chromosome Analysis Suite 1.2.2 from Affymetrix.
Allele peak data and SNP copy numbers were analyzed. The standard bi-allelic genotype calls (AA, AB, BB) do not apply in the tumor's trisomies. The quality metric "MAPD < 25" was fulfilled. According to the manufacturer the quality metrics "SNPQC" and "Waviness SD" do not apply in this solid tumor (http://media.affymetrix.com/support/help/faqs/cytoscan/cytoscan.pdf).
|
| |
|
| Submission date |
Oct 02, 2012 |
| Last update date |
Jun 12, 2015 |
| Contact name |
Jan Menke |
| Organization name |
University Hospital Goettingen
|
| Street address |
Robert-Koch-Strasse 40
|
| City |
Goettingen |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16131 |
| Series (1) |
| GSE41297 |
SNP array data for embryonal rhabdomyosarcoma in a patient with Costello syndrome |
|
