|
| Status |
Public on Dec 18, 2008 |
| Title |
UsiA12_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
U251 glioblastoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
UsiA12 clone derived from the U251 cells stably transfected with the pSuper-p53 and pCI-neo vectors
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated applying the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. The quality and integrity of the total RNA was evaluated with the 2100 Bioanalyzer (Agilent Technologies).
|
| Label |
DIG-UTP
|
| Label protocol |
Digoxigenin-UTP labeled cRNA was generated and amplified from 2 µg of total RNA from each sample using Applied Biosystems Chemiluminescent RT-IVT Labeling Kit v 1.0 (P/N 4340472) according to the manufacturer’s protocol (P/N 4339629).
|
| |
|
| Hybridization protocol |
Array hybridization was performed for 16 hrs at 55 °C. Chemiluminescence detection, image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer (P/N 4338036) following the manufacturer’s protocol (P/N 4339629).
|
| Scan protocol |
Image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer (P/N 4338036) following the manufacturer’s protocol (P/N 4339629).
|
| Description |
mutant p53 as a regulator of transcription
|
| Data processing |
Images were auto-gridded and the chemiluminescent signals were quantified, corrected for background, and finally, spot- and spatially-normalized using the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer software v 1.1 (P/N 4336391). Quantile normalization was done using the limma package within the R environment.
|
| |
|
| Submission date |
Dec 16, 2008 |
| Last update date |
Dec 17, 2008 |
| Contact name |
Genrich Tolstonog |
| E-mail(s) |
genrich.tolstonog@hpi.uni-hamburg.de
|
| Phone |
+49-40-48051235
|
| Fax |
+49-40-48051117
|
| Organization name |
Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology
|
| Department |
Department of Tumor Virology
|
| Street address |
P.O. Box 20 16 52
|
| City |
Hamburg |
| ZIP/Postal code |
D-20206 |
| Country |
Germany |
| |
|
| Platform ID |
GPL1426 |
| Series (1) |
| GSE13991 |
Modulation of gene expression in U251 glioblastoma cells by binding of mutant p53 to intronic and intergenic sequences |
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