|
| Status |
Public on Mar 01, 2011 |
| Title |
GBM_stem_4 days_3 |
| Sample type |
RNA |
| |
|
| Source name |
glioblastoma stem cells, stem, 4 days
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: brain
disease status: glioblastoma
cell type: stem cells G63
|
| Treatment protocol |
glioblastoma stem cells were differentiated in the presence of FCS for 4 days
|
| Growth protocol |
Tumor cells were then 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 plated 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.
|
| Description |
G63_SC.CEL
|
| Data processing |
Data analysis performed using R (2.8.1) and Bioconductor packages. The function rma of package affy (1.20.2) was used for normalization.
|
| |
|
| Submission date |
Mar 10, 2010 |
| Last update date |
Mar 04, 2013 |
| Contact name |
Victor Segura |
| E-mail(s) |
vsegura@unav.es
|
| Organization name |
FIMA
|
| Department |
Unit of Proteomics, Genomics and Bioinformatics
|
| Street address |
Avda. Pío XII, 55
|
| City |
Pamplona |
| State/province |
Navarra |
| ZIP/Postal code |
31008 |
| Country |
Spain |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE20736 |
Microarray analysis of differentiation of human glioblastoma stem cells |
|
| Relations |
| Reanalyzed by |
GSM1092487 |
