|
| Status |
Public on Apr 25, 2011 |
| Title |
RKOAS451 |
| Sample type |
RNA |
| |
|
| Source name |
ATCC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RKOAS451
|
| 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.
|
| Description |
colon cancer cell line
|
| Data processing |
Standard RefRMA pipleline as implemented in APT (Affymetrix Power Tools software) using default settings
|
| |
|
| Submission date |
Apr 12, 2011 |
| Last update date |
Apr 25, 2011 |
| Contact name |
Michael Nebozhyn |
| Organization name |
Merck, Inc
|
| Department |
GpGx/Computational System biology
|
| Street address |
Mail Stop WP53B-120, 770 Sumneytown Pike, Building 53, P.O. Box 4
|
| City |
West Point |
| State/province |
PA |
| ZIP/Postal code |
19486 |
| Country |
USA |
| |
|
| Platform ID |
GPL10379 |
| Series (2) |
| GSE28567 |
EMT is the dominant program in human colon cancer (Affymetrix) |
| GSE28814 |
EMT is the dominant program in human colon cancer |
|
