|
| Status |
Public on Aug 25, 2013 |
| Title |
EPN-135 |
| Sample type |
RNA |
| |
|
| Source name |
brain tumor (ependymoma)
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: brain tumor
tissue: ependymoma
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy (Qiagen) 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 (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
|
| Scan protocol |
GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.
|
| Description |
Gene expression data from surgical tumor sample of ependymoma
[collection protocol] Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )
|
| Data processing |
Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 21,050 genes.
|
| |
|
| Submission date |
Aug 23, 2013 |
| Last update date |
Aug 25, 2013 |
| Contact name |
Andrew M Donson |
| E-mail(s) |
andrew.donson@cuanschutz.edu
|
| Phone |
303 724 4012
|
| Organization name |
CU Anschutz Medical Campus
|
| Department |
Pediatrics
|
| Lab |
RC1 North, P18-4401M
|
| Street address |
12800 E 19th Ave
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80010 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE50161 |
Expression data from human brain tumors and human normal brain |
|
