|
| Status |
Public on Nov 25, 2015 |
| Title |
normal adrenal tissue, donor 3 |
| Sample type |
RNA |
| |
|
| Source name |
normal adrenal tissue
|
| Organism |
Homo sapiens |
| Characteristics |
gender: unknown
histologic type: normal
tumor stage: not applicable
|
| Treatment protocol |
None
|
| Growth protocol |
None
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumor specimens were harvested during surgery and snap frozen in liquid nitrogen to preserve tissue integrity. Tissue samples were classified according to established histopathologic criteria and verified by two independent pathologists. Total RNA was isolated from 50 to 100 mg of pediatric ACT using the RNeasy RNA Midi-Prep kit (Qiagen, Valencia, CA). Tumors were prepared in a 4 degree centigrade cold room, sliced into fine pieces using a sterile scalpel, and homogenized with 18- and 19-gauge needles in lysis Buffer RLT (Qiagen) containing beta-mercaptoethanol.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard one-cycle eukaryote target Affymetrix protocol using 5-10 ug total RNA as starting template (Expression Analysis Technical Manual, 2004, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 20 ug of biotinylated cRNA were hybridized for 16 hr at 45C on the Affymetrix Human Genome HGU133A GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
|
| Data processing |
The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
|
| |
|
| Submission date |
Nov 25, 2015 |
| Last update date |
Nov 25, 2015 |
| Contact name |
Geoffrey Neale |
| E-mail(s) |
geoffrey.neale@stjude.org
|
| Organization name |
St Jude Childrens Research Hospital
|
| Department |
Hartwell Center
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL96 |
| Series (1) |
| GSE75415 |
Gene exrpression profiling of childhood adrenocortical tumors |
|
