|
| Status |
Public on Mar 05, 2013 |
| Title |
GBM_differentiation_4days_3 |
| Sample type |
RNA |
| |
|
| Source name |
Glioblastoma multiforme cells, differentiation, 4 days
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Brain
disease status: Glioblastoma multiforme
patient: G59
cell type: differentiated 4 days
|
| Treatment protocol |
Glioblastoma neurospheres were differentiated in the presence of 10% fetal calf serum and in absence of B-27 supplement for 4days
|
| Growth protocol |
Tumor cells were resuspended in serum-free DMEM/F12 medium (Invitrogen, Carlsbad, CA) containing human recombinant EGF (20 ng/ml; Sigma, St. Louis, MO), bFGF (20 ng/ml; Sigma), B-27 (20 ml per ml of medium; Invitrogen) and heparin (2 mg/ml), and seeded at a density of 3x106 live cells/60-mm plate
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
|
| Label |
Biotin
|
| Label protocol |
The cDNA was prepared from 5 microg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthezising the cRNA using the IVT labeling kit (Affimetrix). The synthezised cRNA was purified with the GeneChip Sample Cleanup Module (Affimetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133A 2.0 chip according to the protocols provided by the manufacturer.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
|
| Data processing |
Data analysis performed using R (2.15.0) and Bioconductor packages. The function rma of package affy (1.36.0) was used for normalization
|
| |
|
| Submission date |
Mar 04, 2013 |
| Last update date |
Mar 05, 2013 |
| Contact name |
Raquel Malumbres |
| E-mail(s) |
rmalumbres@yahoo.com
|
| Phone |
+34 948194700
|
| Organization name |
University of Navarra/ Clínica Universidad de Navarra
|
| Department |
Hemato-Oncology
|
| Lab |
Multiple Myeloma
|
| Street address |
Avenida Pio XII 55
|
| City |
Pamplona |
| State/province |
Navarra |
| ZIP/Postal code |
31008 |
| Country |
Spain |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE44841 |
Microarray analysis of differentiation of human glioblastoma neurospheres |
| GSE44843 |
Involvement of miRNAs in the Differentiation of Human Glioblastoma Multiforme Brain Tumor Stem-Like Cells |
|
