|
| Status |
Public on Jun 04, 2009 |
| Title |
RMS-YM,Embryonal,rhabdomyosarcoma cell line |
| Sample type |
RNA |
| |
|
| Source name |
RMS-YM
|
| Organism |
Homo sapiens |
| Characteristics |
Cell line from a rhabdomyosarcoma tumor
|
| Biomaterial provider |
T. Naoe, Nagoya University School of Medicine, Japan
|
| Growth protocol |
RMS-YM cells were cultured in RPMI (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 protocol
|
| Description |
RMS-YM cells were grown under standard conditions and harvested at 70%
confluency. Total RNA was isolated and analyzed on Affymetrix U133
Plus 2.0 to generate expression profiles.
|
| Data processing |
Expression data (.cel files) were normalized with the MAS5.0 algorithm
(target signal = 100) using GCOS software (Affymetrix)
|
| |
|
| Submission date |
Aug 21, 2007 |
| Last update date |
Aug 28, 2018 |
| 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) |
| GSE8840 |
Effect of genomic imbalances on gene expression in rhabdomyosarcoma |
|
| Relations |
| Reanalyzed by |
GSE119087 |
