|
| Status |
Public on Dec 01, 2011 |
| Title |
Xenograft 2339, biological rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
GBM Subcutaneous Xenograft
|
| Organism |
Homo sapiens |
| Characteristics |
batch: 5
date of array: 2
line number: 31
line type: Subcutaneous Xenograft
xenograft line: 2339
|
| Growth protocol |
Xenograft lines grown SC or IC until 200 mm^3, cell lines cultured to 70% confluence in either serum free or serum containing media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Qiagen midi (xenograft), or mini (cell lines) kits. Xenograft tissue pulverized in liquid nitrogen and homogenized using a rotor-stator homogenizer
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2ug of Total RNA (ExpressionAnalysis Techinical Manual, 2005, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10ug of biotinylated cRNA was hybridized for 16hr at 45C onto the Affymetrix Human Genome U133A Plus 2.0 Array. Gene Chips were washed and stained in the Affymetrix Fluidics Station 450 according to standard protocols.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
|
| Data processing |
data normalized using Bioconductor in R using either RMA or MAS5.0 normalization protocols (RMA provided, see website for MAS5). Batch corrected expression values calculated by factor regression across Affymetrix doping and housekeeping controls
|
| |
|
| Submission date |
Dec 29, 2010 |
| Last update date |
Dec 01, 2011 |
| Contact name |
Jason W Reeves |
| E-mail(s) |
jwr11@duke.edu
|
| Organization name |
Duke University
|
| Lab |
Nevins, Joseph
|
| Street address |
101 Science Dr
|
| City |
Durham |
| State/province |
North Carolina |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL571 |
| Series (1) |
| GSE26344 |
In vitro models of glioblastoma (GBM) |
|
