|
| Status |
Public on Nov 02, 2007 |
| Title |
Melanoma (AF500KNSPSKMEL5) |
| Sample type |
genomic |
| |
|
| Source name |
SKMEL5 Cell Line
|
| Organism |
Homo sapiens |
| Characteristics |
Melanoma
|
| Growth protocol |
Cells were grown in in RPMI 1640 supplemented with 10% heat-inactivated FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from cultured cells with Mini DNeasy kit (Qiagen, Inc.)
|
| Label |
biotin
|
| Label protocol |
250 ng Genomic DNA was biotinylated as described by manufacturer (Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix).
|
| |
|
| Hybridization protocol |
Hybridizations were performed according to the standard manufacturer's describe in Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix.
|
| Scan protocol |
Scanning was done using an Affymetrix 3000 microarray scanner. Specifications can be found in Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix
|
| Description |
Melanoma
|
| Data processing |
Image files were analyzed using the dChip software. A panel of chips (n = 12) assayed with germline DNA served as a reference in order to calculate a test/reference ratio. The ratios were then subject global normalization that assumed that the median copy number is diploid (2n; log2 Ratio = 0).
|
| |
|
| Submission date |
May 09, 2007 |
| Last update date |
Oct 31, 2007 |
| Contact name |
Joel Greshock |
| Organization name |
GlaxoSmithKline
|
| Department |
Translational Medicine, Oncology
|
| Street address |
2301 Renaissance Blvd.
|
| City |
King of Prussia |
| State/province |
PA |
| ZIP/Postal code |
19406 |
| Country |
USA |
| |
|
| Platform ID |
GPL3718 |
| Series (1) |
| GSE7822 |
A comparison of DNA copy number profiling platforms using a panel of melanoma cell lines |
|
