|
| Status |
Public on Jul 04, 2012 |
| Title |
D425-shOTX2_2, t=16 |
| Sample type |
RNA |
| |
|
| Source name |
D425
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Medulloblastoma cell line D425
protocol: doxycyline inducible shRNA against OTX2
time: 16 hrs
time course: 2
|
| Treatment protocol |
D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.
|
| Growth protocol |
Cells were cultured in MEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
|
| Label |
biotin
|
| Label protocol |
RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
|
| |
|
| Hybridization protocol |
10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
|
| Scan protocol |
Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco
|
| Description |
NB163
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Data processing |
Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)
|
| |
|
| Submission date |
Jul 11, 2010 |
| Last update date |
Jul 04, 2012 |
| Contact name |
Richard Volckmann |
| E-mail(s) |
r.volckmann@amsterdamumc.nl
|
| Organization name |
Academic Medical Centre, University of Amsterdam
|
| Department |
Department of Oncogenomics
|
| Street address |
P.O. Box 22700
|
| City |
Amsterdam |
| ZIP/Postal code |
1100DE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE22875 |
OTX2 drives medulloblastoma proliferation via direct regulation of cell cycle genes and inhibits differentiation |
|
