|
| Status |
Public on Oct 10, 2015 |
| Title |
639761_13608_1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Tumor
|
| Organism |
Homo sapiens |
| Characteristics |
mutation status: BRAF V600E
tissue: melanoma
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using sodium thiocyanate as described in Wilson et al. Clinical Cancer Research 20(12):3328-37, 2014.
|
| Label |
Cy5
|
| Label protocol |
Tumor DNA was labeled using BioPrime® Array CGH Genomic Labeling System (Life Technologies, Grand Island, NY) according to manufacturer’s instructions
|
| |
|
| Channel 2 |
| Source name |
Pooled Normal
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
sample type: reference
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using sodium thiocyanate as described in Wilson et al. Clinical Cancer Research 20(12):3328-37, 2014.
|
| Label |
Cy3
|
| Label protocol |
Tumor DNA was labeled using BioPrime® Array CGH Genomic Labeling System (Life Technologies, Grand Island, NY) according to manufacturer’s instructions
|
| |
|
| |
| Hybridization protocol |
Array-based comparative genomic hybridization (aCGH) was performed using the Agilent SurePrint G3 Human CGH 2x400K M microarrays following manufacturer’s instructions
|
| Scan protocol |
Scanned on Agilent scanner
|
| Data processing |
Images were quantified using Agilent Feature Extraction Software and extracted data were analyzed using BioDiscovery’s Nexus 7 copy-number software (Nexus Genomics Inc.)
|
| |
|
| Submission date |
Oct 09, 2015 |
| Last update date |
Oct 10, 2015 |
| Contact name |
Katherine Nathanson |
| E-mail(s) |
knathans@exchange.upenn.edu
|
| Organization name |
Perelman School of Medicine at the University of Pennsylvania
|
| Street address |
421 Curie Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19103 |
| Country |
USA |
| |
|
| Platform ID |
GPL9777 |
| Series (1) |
| GSE73899 |
Copy number analysis in melanoma tumor samples from E2603 |
|
