|
| Status |
Public on Aug 28, 2015 |
| Title |
PDAC53 |
| Sample type |
RNA |
| |
|
| Source name |
frozen pancreatic tissue
|
| Organism |
Homo sapiens |
| Characteristics |
overall survival (month): 15.5
vital.status: DEAD
Stage: 2B
|
| 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 |
The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin. After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency. The labeled molecules are biotinylated-cRNA.
|
| |
|
| 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 45C 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 |
frozen pancreatic tissue
|
| Data processing |
Expression values were calculated using the robust multi-array average (RMA) algorithm
|
| |
|
| Submission date |
May 09, 2014 |
| Last update date |
Aug 28, 2015 |
| Contact name |
Dung-Tsa Chen |
| E-mail(s) |
dung-tsa.chen@moffitt.org
|
| Organization name |
Moffitt Cancer Center
|
| Department |
Biostatistics and Bioinformatics
|
| Street address |
12902 Magnolia Drive
|
| City |
Tampa |
| State/province |
FL |
| ZIP/Postal code |
33647 |
| Country |
USA |
| |
|
| Platform ID |
GPL15048 |
| Series (1) |
| GSE57495 |
Development of a prognostic gene signature in pancreatic cancer |
|
