|
| Status |
Public on Sep 27, 2012 |
| Title |
Tumor 3_4C @ 30mins |
| Sample type |
RNA |
| |
|
| Source name |
Tumor 3_4C @ 30mins
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: VHL Clear Cell Renal Cell Carcinoma
patient: Tumor 3
treatment: 4C @ 30mins
|
| Treatment protocol |
10 renal tumors were divided and treated under the above listed conditions and snap frozen at 5, 30, 60, 120 and 240 minutes after surgical resection
|
| 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 from 100ng total RNA using GeneChip Two-Cycle cDNA Target Synthesis Kit (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 plus 2.0 olgionucleotide array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
Each array was washed, stained and scanned by the Affymetrix GeneChip 3000 Scanner. Raw intensities for each probe were stored as .DAT and .CEL files by the GeneChip Operating Software v1.4 (Affymetrix Inc, Santa Clara, CA USA).
|
| Description |
Gene expression data from tumor 3 at ischemic conditions
|
| Data processing |
Complete analyses of array data were carried out in BRB-Array Tools v3.7 (http://linus.nci.nih.gov/BRB-ArrayTools.html)
Processed/Filtered and Log2_transformed array intensities
|
| |
|
| Submission date |
Sep 25, 2012 |
| Last update date |
Sep 27, 2012 |
| Contact name |
Nick Liu |
| E-mail(s) |
nick.liu@gmail.com
|
| Organization name |
Indiana University Hospital
|
| Department |
Department of Urology
|
| Street address |
535 Barnhill Drive Suite 420
|
| City |
INDIANAPOLIS |
| State/province |
Indiana |
| ZIP/Postal code |
46202 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE41137 |
Impact of Ischemia and Procurement Conditions on Gene Expression in Renal Cell Carcinoma |
|
