|
| Status |
Public on May 26, 2009 |
| Title |
WW165, primary melanoma, rep2 |
| Sample type |
RNA |
| |
|
| Source name |
primary melanoma
|
| Organism |
Homo sapiens |
| Characteristics |
Gender: female
Age: 62 year
|
| Growth protocol |
Melanoma cells from primary melanoma were excised from tumor samples and used during the fifth passage in culture in OptiMEM with antibiotics, 5% fetal calf serum (regular medium) and growth supplements. Samples were collected with participants’ informed consent according to Health Insurance Portability and Accountability Act (HIPAA) regulations with Human Investigative Committee protocol.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Approximately 20–30 million cells (normal human melanocytes and melanoma cells/each) were used for mRNA extraction. High-quality total RNA was prepared with the TRIzol reagent (Invitrogen Life Technologies, Inc., Invitrogen Corp., Carlsbad, CA). The quality of RNA products was determined visually by 1% denaturing agarose gel, and RNA concentration was measured using a spectrophotometer. Poly(A) mRNA was further isolated from 150-300 µg total RNA/sample using the PolyATtract mRNA isolation system IV (Pro-mega, Madison, WI) following the manufacturer’s instructions, and reversed transcribed to double stranded cDNA. This additional step is required to eliminate the melanin present in the total RNA preparation that suppresses PCR hybridization reactions.
|
| Label |
Cy3
|
| Label protocol |
Standard Nimblegen Protocol.
|
| |
|
| Hybridization protocol |
Standard Nimblegen Protocol, performed by Nimblegen.
|
| Scan protocol |
Standard Nimblegen Protocol, performed by Nimblegen.
|
| Description |
Genome-wide gene expression of WW165 primary melanoma is determined. This data was used in association with genome-wide promoter methylation data available in this GEO series.
|
| Data processing |
The qspline normalization method (Workman et al., 2002) was used to normalize a set of single channels hybridization derived from a two channel platform. In particular, the qspline implementation available in the affy Bioconductor was used (http://www.bioconductor.org/).
|
| |
|
| Submission date |
Nov 20, 2008 |
| Last update date |
May 26, 2009 |
| Contact name |
Ruth Halaban |
| E-mail(s) |
ruth.halaban@yale.edu
|
| Organization name |
Yale University
|
| Department |
Dermatology
|
| Street address |
15 York St.
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06520 |
| Country |
USA |
| |
|
| Platform ID |
GPL6602 |
| Series (1) |
| GSE13706 |
Genome-Wide Screen of Promoter Methylation Identifies Novel Markers for Tumor Development in Melanoma |
|
