|
| Status |
Public on Feb 27, 2015 |
| Title |
PA_0519_1 |
| Sample type |
RNA |
| |
|
| Source name |
PA_0519_1
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: brain tumor
tissue: pilocytic astrocytoma
|
| Extracted molecule |
total RNA |
| Extraction protocol |
[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 )
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 |
reanalysis of GSM1214955
|
| 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. This list was further filtered to remove probe sets that were expressed below a threshold level that denoted absence of expression in any sample.
|
| |
|
| Submission date |
Feb 27, 2015 |
| Last update date |
Feb 27, 2015 |
| 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) |
| GSE66354 |
Investigation of the mechansim underlying the inflammatory phenotype in Group A ependymoma |
|
| Relations |
| Reanalysis of |
GSM1214955 |
