|
| Status |
Public on Dec 01, 2010 |
| Title |
Melanoma cell line_WM35 |
| Sample type |
RNA |
| |
|
| Source name |
Melanoma Cell Line
|
| Organism |
Homo sapiens |
| Characteristics |
histological subtype: Primary superficial spreading melanoma
cell line: Melanoma cell line, WM35
|
| 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 |
total RNA |
| Extraction protocol |
RNA was isolated from melanoma cell lines using RNAeasy columns (Qiagen, Valencia, CA), and the quality and quantity assessed by UV spectrophotometer.
|
| Label |
biotin
|
| Label protocol |
Affymetrix One-cycle Labeling kit and instructions in the Affymetrix GeneChip Expression Analysis Technical Manual were used.
|
| |
|
| Hybridization protocol |
Standard Affymetrix Hybridization Protocol as recommended by the Affymetrix GeneChip Expression Analysis Technical Manual was used.
|
| Scan protocol |
Affymetrix GeneArray Scanner 3000 7G
|
| Description |
Gene expression data
|
| Data processing |
Array data were normalized using the robust multichip average (RMA) and filtered for expression values lower than 16. Data were then log transformed to perform an analysis of variance (ANOVA) and a two-sample unpaired t-test with p-values adjusted for multiple comparisons (Boferroni correction). A single factor, two-level ANOVA design was utilized to examine sources of measured variability and identify differences between the SSM (WM1552c, WM35) and NM cell line (WM39, WM278, LU451, SK-MEL-147) groups. A software package dChip was used to facilitate the analysis.
|
| |
|
| Submission date |
Jun 11, 2010 |
| Last update date |
Jun 11, 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 |
GPL571 |
| Series (2) |
| GSE22301 |
Gene expression data from melanoma cell lines and melanocyte controls |
| GSE22306 |
Integrative genomics identifies molecular alterations that differentiate superficial spreading and nodular melanoma |
|
