|
| Status |
Public on Oct 21, 2010 |
| Title |
Immortalized melanocyte_Hermes1 [SNP] |
| Sample type |
genomic |
| |
|
| Source name |
Immortalized melanocyte_Hermes1
|
| Organism |
Homo sapiens |
| Characteristics |
histological subtype: Immortalized melanocyte
cell line: Immortalized melanocyte, Hermes1
|
| Treatment protocol |
None
|
| Growth protocol |
Cell lines derived from primary tumors were cultured in Mel 2% medium (Fang et al.Cancer Res, 2005. PMID 16230395), and metastatic cell lines were cultured as previously described (Segura et al. Proc Natl Acad Sci USA, 2009. PMID 19188590 ).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Melanoma and melanocyte DNA was extracted using the Qiagen QIAmp DNA Mini kit (Qiagen Valencia, CA). DNA quantity was assessed by UV spectrophotometry and quality was assayed by agarose gel electrophoresis.
|
| Label |
biotin
|
| Label protocol |
As per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR purified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Description |
Hybridized to SNP6.0 Arrays
|
| Data processing |
CEL files were generated using the GeneChip Command Console software (Affymetrix), and the Birdseed v2 algorithm (Korn et al. Nat Genet, 2008. PMID 18776909) was used to make the genotype calls and summarize the probe-set intensity (SPI) values for ensuing copy number analysis. A single normal reference genome profile assayed in the same batch was created using values from the 2 normal melanocytes cultured from infant foreskin (HEM-N and HEM-LP).
Primary data description: 1. 22 CHP files for melanoma and melanocyte cell lines 2. Data table that includes the Genotype Call (AA, AB, BB, NC, and NoCall) and the intensity signal for signal A and signal B in 22 cell lines.
|
| |
|
| Submission date |
Jun 11, 2010 |
| Last update date |
Oct 21, 2010 |
| Contact name |
Iman Osman |
| E-mail(s) |
iman.osman@nyumc.org
|
| Phone |
212-263-9089
|
| Fax |
212-263-9090
|
| Organization name |
New York University School of Medicine
|
| Department |
Urology
|
| Street address |
522 First Avenue, SML405
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL6801 |
| Series (2) |
| GSE22305 |
Clinical relevance of SKP2 alterations in metastatic melanoma |
| GSE22306 |
Integrative genomics identifies molecular alterations that differentiate superficial spreading and nodular melanoma |
|
