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Sample GSM672046 Query DataSets for GSM672046
Status Public on Feb 06, 2014
Title Sotos 2
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

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
1007_s_at 8.881828452
1053_at 6.807847916
117_at 4.604590653
121_at 8.51325855
1255_g_at 3.559242484
1294_at 6.83969572
1316_at 4.983073086
1320_at 5.939603028
1405_i_at 3.41434459
1431_at 3.498115819
1438_at 6.468632695
1487_at 7.522837653
1494_f_at 5.996182113
1552256_a_at 7.095558262
1552257_a_at 8.132447556
1552258_at 4.165285116
1552261_at 3.494451894
1552263_at 6.405420822
1552264_a_at 8.00964398
1552266_at 4.163504489

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM672046_071009MJA_U133+2.0_RVi10.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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