|
| Status |
Public on Mar 15, 2012 |
| Title |
experiment 44, GFP transduced |
| Sample type |
RNA |
| |
|
| Source name |
primary cultured skeletal muscle, control
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: paravertebral muscles biopsies
transfection: adenovirus containing GFP
experiment: 44
|
| Treatment protocol |
Differentiated cultured muscle cells were transduced with adenoviruses containing PGC-1alpha or GFP.
|
| Growth protocol |
Cells were grown at 37ºC and 5% CO2 conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the QIAGEN Rneasy kit, treated with DNase, and homogenized with a Polytron. Quality of samples were monitored with an Agilent 2100 Bioanalyzer.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared using the Illumina Amplification kit (Ambion).
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol.
|
| Scan protocol |
Illumina BeadScan software.
|
| Description |
C44.GFP
|
| Data processing |
Raw data was extracted, background corrected and summarized using BeadStudio data analysis software. Statistical analysis was carried out with Bioconductor. The lumi package was used to apply log2 transformation followed by quantile normalization to the BeadStudio summarized data. Then, a paired t-test was conducted with Limma to select differentially expressed genes between the PGC-1alpha-overexpressers and controls. Only those genes with a p value smaller than 0.025 and a fold change greater than 1.5 were selected.
|
| |
|
| Submission date |
Mar 28, 2011 |
| Last update date |
Mar 15, 2012 |
| Contact name |
Sergi Beltran |
| Organization name |
Universitat de Barcelona
|
| Department |
Serveis Cientificotècnics
|
| Lab |
Unitat de Bioinformàtica
|
| Street address |
Baldiri Reixac 10
|
| City |
Barcelona |
| ZIP/Postal code |
08028 |
| Country |
Spain |
| |
|
| Platform ID |
GPL6884 |
| Series (1) |
| GSE28206 |
Analysis of PGC-1alpha overexpression effects on the whole transcriptome in cultured skeletal muscle cells |
|
