|
| Status |
Public on Jul 06, 2012 |
| Title |
SJMB087 |
| Sample type |
RNA |
| |
|
| Source name |
Medulloblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
subgroup: G3
age: 3yrs 2mos
Sex: Male
ethnic: Hispanic
m stage: MB-AN
|
| Treatment protocol |
all samples are untreated tissues
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Isolation was performed using RNA STAT-60, according to the manufacturer's instructions. Briefly, tissue samples were homogenized in the STAT-60 using teflon homogenizers. Chloroform was added and the samples centrifuged. The upper layer (aqueous phase) was removed to a fresh tube and the RNA precipitated with isopropanol. Following centrifugation, the RNA pellet was washed once in 75% ethanol, then the air-dried pellet resuspended in DEPC-treated water.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix Two-Cycle protocol from 100 ng of total RNA (Expression Analysis Technical Manual, 2005-2006, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 v2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000 7G.
|
| Description |
primary tumor
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Natural log start stransfomation was perfomed in STATA/SE 11.2.
|
| |
|
| Submission date |
Apr 19, 2012 |
| Last update date |
Jan 08, 2019 |
| Contact name |
David Finkelstein |
| E-mail(s) |
[email protected]
|
| Phone |
9014953931
|
| Organization name |
St Jude Children's Research Hospital
|
| Department |
Computational Biology
|
| Street address |
332 N. Lauderdale St.
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE37418 |
Novel mutations target distinct subgroups of medulloblastoma. |
|
| Relations |
| Reanalyzed by |
GSE124814 |
