|
| Status |
Public on Oct 01, 2008 |
| Title |
A673 cells treated with control siRNA, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
A673 cell line, a human EWS/FLI translocated Ewing tumor cell line
|
| Organism |
Homo sapiens |
| Characteristics |
treated A673 Ewing tumor cell line
|
| Biomaterial provider |
ATCC
|
| Treatment protocol |
A673 cells were treated for 24 hours either with 100 nM Trichostatin A (TSA) or 0.01% DMSO. In siRNA experiments A673 cells were resuspended in medium containing 5 nM siRNA and transfection reagent and incubated for 48 hours. RNA from cells under such treatment was isolated.
|
| Growth protocol |
Cells were cultivated in RPMI 1640 medium containing 10 % FCS with additional 1 % penicillin/streptomycin in a humidified atmosphere at 37 °C and 5 % CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At 80 % confluency of the cells, total RNA was prepared with acid phenol/chloroform extraction (TRIzol, Invitrogen; Karlsruhe, Germany) followed by purification with RNeasy Mini Kit (Qiagen; Hilden, Germany) according to the manufacturer’s instructions and was quantified spectro-photometrically. The quality of the purified RNA was assessed by agarose gel analysis.
|
| Label |
biotin, streptavidin-phycoerytrin
|
| Label protocol |
A total of 10 µg RNA from each sample was used to prepare biotinylated target cRNA as previously described (Staege MS, Hutter C, Neumann I, et al. DNA microarrays reveal relationship of Ewing family tumors to both endothelial and fetal neural crest-derived cells and define novel targets. Cancer Res 2004;64:8213-21). A detailed protocol is available at www.affymetrix.com.
|
| |
|
| Hybridization protocol |
Affymetrix
|
| Scan protocol |
Affymetrix
|
| Description |
A673 cells were treated for 24 hours either with 100 nM Trichostatin A (TSA) or 0.01% DMSO. In siRNA experiments A673 cells were resuspended in medium containing 5 nM siRNA and transfection reagent and incubated for 48 hours. RNA from cells under such treatment was isolated with Trizol and subjected to microarray analysis onto human U133A microarray following the Affymetrix protocol.
|
| Data processing |
Microarray Suite 5.0 was used with the data and for normalization by scaling all probe sets to 500.
|
| |
|
| Submission date |
Sep 07, 2008 |
| Last update date |
Sep 08, 2008 |
| Contact name |
Guenther HS Richter |
| E-mail(s) |
guenther.richter@charite.de
|
| Organization name |
Charité - Universitätsmedizin Berlin
|
| Department |
Department of Pediatrics, Division of Oncology and Hematology
|
| Street address |
Augustenburger Platz 1
|
| City |
Berlin |
| ZIP/Postal code |
D-13353 |
| Country |
Germany |
| |
|
| Platform ID |
GPL96 |
| Series (1) |
| GSE12692 |
EZH2 is a mediator of EWS-FLI1 driven tumor growth blocking endothelial and neuro-ectodermal differentiation |
|
