|
| Status |
Public on Mar 10, 2007 |
| Title |
Non-tumorigenic (PE15NTG_B) |
| Sample type |
RNA |
| |
|
| Source name |
non-tumorigenic breast tumor
|
| Organism |
Homo sapiens |
| Characteristics |
non-tumorigenic breast tumor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized according to the manufacturer's instructions.
|
| Scan protocol |
none
|
| Description |
Non-tumorigenic population of a breast tumor isolated using fluorescence activated cell sorting. Sample consists of three replicates.
|
| Data processing |
To obtain an expression measure for a given probeset, the mismatch hybridization values were subtracted from the perfect match values, and the average of the middle 50% of these differences was used as the expression measure for the probe set. A quantile normalization procedure was then applied to adjust for differences in the probe intensity distribution across different chips. Specifically, we applied a monotone linear spline to each chip that mapped quantiles 0.01 up to 0.99 (in increments of 0.01) exactly to the corresponding quantiles of a standard chip. The transform log2 [200 + max(X;0)] was then applied.
|
| |
|
| Submission date |
Jan 26, 2007 |
| Last update date |
Mar 09, 2007 |
| Contact name |
Xinhao Wang |
| E-mail(s) |
xinhao.wang@oncomed.com
|
| Phone |
650-995-8211
|
| Organization name |
OncoMed Pharmaceuticals Inc
|
| Street address |
800 Chesapeake
|
| City |
Redwood City |
| State/province |
CA |
| ZIP/Postal code |
94063 |
| Country |
USA |
| |
|
| Platform ID |
GPL97 |
| Series (1) |
| GSE6883 |
The prognostic role of a gene signature from tumorigenic breast-cancer cells. |
|
