|
| Status |
Public on Mar 18, 2011 |
| Title |
secondary glioblastoma_2 |
| Sample type |
RNA |
| |
|
| Source name |
brain tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: secondary brain tumor
cell type: glioblastoma
age: 13
gender: male
tumor grade: IV
|
| Treatment protocol |
No treatment.
|
| Growth protocol |
Human glioblastoma cells were cultured in DMEM supplemented with 10% FCS and standard antibiotics in an incubator at 37°C and 5% CO2 humidified atmosphere.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the primary tumor samples using Trizol reagent, according to manufacturer’s instructions, and resuspended in diethylpyrocarbonate (DEPC) treated water. Total RNA was further purified using the RNeasy kit (Qiagen) and following the protocol for Total RNA cleanup. Cultured cells were collected when plates were 70-80% confluent and RNA was extracted using RNeasy Mini kit (Qiagen).
|
| Label |
Biotin
|
| Label protocol |
RNA was then amplified and labelled using the Affymetrix 2-cycle amplification protocol as per manufacturer’s instructions (Affymetrix).
|
| |
|
| Hybridization protocol |
Samples were hybridized to Affymetrix U133v2.0 GeneChips and scanned as per manufacturer’s instructions.
|
| Scan protocol |
Chips were scanned using an Affymetrix GeneChip scanner.
|
| Description |
bh20061208u133v2_A_30-2ary-GBM3_1
|
| Data processing |
Expression values were estimated using the GC-RMA implementation found in Genedata’s Refiner 4.1 (Genedata) package. Data-mining and visualization was performed using Genedata’s Analyst 4.1 package. Only median fold ratio values with P < 0.05 using t test were used for subsequent analysis. All samples were quintile normalized and median scaled to correct for minor variations in their expression distributions.
|
| |
|
| Submission date |
Apr 24, 2009 |
| Last update date |
Jun 26, 2012 |
| Contact name |
Michal Grzmil |
| E-mail(s) |
michal.grzmil@fmi.ch
|
| Phone |
+41 61-6978565
|
| Fax |
+41-61-6973976
|
| Organization name |
Friedrich Miescher Institute for Biomedical Research
|
| Department |
Growth control
|
| Lab |
3.46
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE15824 |
Gene expression profiling of human gliomas and human glioblastoma cell lines |
|
