|
| Status |
Public on Aug 24, 2007 |
| Title |
SKNAS-NmycER, t=24 hrs |
| Sample type |
RNA |
| |
|
| Source name |
SKNAS-NmycER cells
|
| Organism |
Homo sapiens |
| Characteristics |
Cell line from neuroblastoma tumor, stably transfected with NmycER expression vector
|
| Biomaterial provider |
Human Genetics, Academic Medical Centre, Amsterdam
|
| Treatment protocol |
To activate Nmyc-ER in SKNAS-NmycER, 4-hydroxy-tamoxifen was added to the medium to a final concentration of 50 nmol/l.
|
| Growth protocol |
SKNAS-NmycER cells were cultured in DMEM (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. Labelling 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 protocol.
|
| Description |
SKNAS-NmycER cells were grown under standard conditions and harvested at diferent timepoints after addition of 4-hydroxytamoxifen. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.
|
| Data processing |
Expression data (.cel files) were normalized with the MAS5 algorithm (target signal = 100) using GCOS software (Affymetrix).
|
| |
|
| Submission date |
Jun 08, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Linda Valentijn |
| 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) |
| GSE8066 |
Dickkopf-1 is down-regulated by MYCN and inhibits neuroblastoma cell proliferation |
|
| Relations |
| Reanalyzed by |
GSE64985 |
| Reanalyzed by |
GSE119087 |
