|
| Status |
Public on Sep 08, 2015 |
| Title |
GBM_EGFRvIIIpos 7 |
| Sample type |
RNA |
| |
|
| Source name |
Brain tissue
|
| Organism |
Homo sapiens |
| Characteristics |
egfrviii statue: +
tissue: primary GBM tumor
|
| Treatment protocol |
tissue harvested from standard image-guided surgical resections and banked between January 2002 and January 2009 at the Hospital of the University of Pennsylvania
|
| Growth protocol |
From human patients
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Briefly, ~1 μg of total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase (Life Technologies) primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription to generate labeled cRNAs.
|
| Label |
biotin
|
| Label protocol |
The cRNAs were subjected to hybridization at 45oC for 16 hrs, followed by washing, staining, and scanning of the chip according to the manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
The cRNAs were subjected to hybridization at 45oC for 16 hrs, followed by washing, staining, and scanning of the chip according to the manufacturer’s instructions.
|
| Scan protocol |
A confocal scanner was used to collect fluorescence signal at 3 μm resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.
|
| Data processing |
Affymetrix Microarray Suite 5.0 was used to quantify expression levels for targeted genes. The raw data were subjected to quantile normalization to reduce the signal to noise ratio due to tumor heterogeneity. The default values provided by Affymetrix were applied to all analysis parameters.
|
| |
|
| Submission date |
Sep 20, 2013 |
| Last update date |
Sep 08, 2015 |
| Contact name |
Matthew J Lazzara |
| Organization name |
University of Pennsylvania
|
| Street address |
220 South 33rd Street
|
| City |
Philadelphia |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE51062 |
Expression data from human GBMs |
|
