|
| Status |
Public on Feb 06, 2014 |
| Title |
Sotos 1 |
| Sample type |
RNA |
| |
|
| Source name |
Human dermal fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: dermal fibroblasts
treatment: untreated
disease state: Sotos syndrome with NSD1 abnormality
|
| Treatment protocol |
At reaching 80-90% monolayer confluency cells were stimulated with retinoic acid at a final concentration of 10-6M for 48h. Because of the light-sensitivity of RA, cell cultures were kept in the dark.
|
| Growth protocol |
Skin fibroblasts were cultured in Dulbecco’s modified Eagle’s Medium supplemented with glutamax and containing 10% fetal calf serum, 50IU/ml penicillin and 50μg/ml streptomycin. Medium was changed twice a week and cells were split at a ratio of 1:6 upon reaching monolayer confluence. The cell cultures were maintained at 37oC in a humidified atmosphere of 5% CO2 and 95% O2. In all experiments cell passages were between 2 and 10.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed with the Nucleospin RNA II kit (Macherey-Nagel, Dϋren, Germany).
|
| Label |
biotin
|
| Label protocol |
Generation of cDNA, cRNA, and biotin-labeling were performed by ServiceXS Leiden according to manufacturer’s guidelines (Affymetrix, Santa Clara, CA, USA).
|
| |
|
| Hybridization protocol |
Hybridization was performed by the Leiden Genome Technology Center following manufacturer’s protocols (Affymetrix, Santa Clara, CA, USA)
|
| Scan protocol |
Scanning was performed by the Leiden Genome Technology Center ollowing manufacturer’s protocols (Affymetrix, Santa Clara, CA, USA)
|
| Description |
Gene expression data from fibroblasts from a Sotos syndrome patient
|
| Data processing |
Analyses of the microarray expression data were made in R (version 2.7.0; www.r-project.org). Probe level data was preprocessed with the Robust Multi-array Average (RMA) algorithm in the Bioconductor (www.bioconductor.org) affy package (version 1.18.2).
|
| |
|
| Submission date |
Feb 09, 2011 |
| Last update date |
Feb 06, 2014 |
| Contact name |
Remco Visser |
| Organization name |
Leiden University Medical Center
|
| Department |
Department of Pediatrics, J6-S
|
| Street address |
Albinusdreef 2
|
| City |
Leiden |
| ZIP/Postal code |
P.O. Box 9600 |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE27200 |
Expression data from Sotos syndrome patients and controls |
|
