|
| Status |
Public on Jul 10, 2014 |
| Title |
SUM149PT |
| Sample type |
RNA |
| |
|
| Source name |
breast cancer cell line SUM149PT
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SUM149PT
cell type: Breast Cancer
|
| Biomaterial provider |
ATCC
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Cell lines were grown as recommended by vendor ATCC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.
|
| Label |
Biotin
|
| Label protocol |
Nugen amplification protocol
|
| |
|
| Hybridization protocol |
GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45oC with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.
|
| Scan protocol |
Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.
|
| Data processing |
Standard RMA pipleline as implemented in APT (Affymetrix Power Tools software) using default settings
|
| |
|
| Submission date |
Jul 09, 2014 |
| Last update date |
Jul 10, 2014 |
| Contact name |
Sergey Lezhnin |
| E-mail(s) |
sergey_lezhnin@merck.com
|
| Organization name |
Merck Research Laboratories
|
| Department |
Molecular Profiling
|
| Lab |
Data Analysis
|
| Street address |
33 AVENUE LOUIS PASTEUR
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL10379 |
| Series (1) |
| GSE59242 |
Profiling of human cancer breast cell lines (Affymetrix) |
|
