|
| Status |
Public on Jun 16, 2014 |
| Title |
PGC1a OV, biol. rep. 3 |
| Sample type |
RNA |
| |
|
| Source name |
C2C12 cells with PGC1a OV
|
| Organism |
Mus musculus |
| Characteristics |
differentiation stage: C2C12 myotubes
phenotype: PGC-1alpha over-expression
|
| Treatment protocol |
The myotubes were grown in the presence of either GFP control adenovirus (condition 1) or PGC-1alpha expressing adenovirus (condition 2) for 48h.
|
| Growth protocol |
C2C12 cells were grown to 90% confluence in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 Units/ml penicillin and 100ug/ml streptomycin. The differentiation to myotubes was induced by changing the medium to DMEM supplemented with 2% horse serum for 72h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA was extracted using Trizol® and according to the Trizol® Reagent RNA extraction protocol.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNA were prepared according to the WT Expression Kit (Ambion) followed by the WT Terminal Labeling and Hybridization Labeling Kit (Affymetrix) from 200ng total RNA
|
| |
|
| Hybridization protocol |
3 µg of fragmented cRNA were hybridized for 17 hr at 45°C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Fluidics Station 450 (Affymetrix) under FS450_0002 protocol, using the Hybridization Wash and Stain Kit (Affymetrix)
|
| Scan protocol |
The GeneChips were scanned with an Affymetrix GeneChip Scanner 3000 7G
|
| Data processing |
Raw probe intensities were corrected for background and unspecific binding using the Bioconductor package “affy”. Probes were classified as expressed or non-expressed by using the “Mclust” R package and, after removal of non-expressed probes, the intensity values were quantile normalized across all samples. Using mapping of the probes to the UCSC collection of mouse mRNAs, probes were then associated to a comprehensive collection of mouse promoters available from the SwissRegulon database (Pachkov et al., 2013). The log2 expression level of a given promoter was calculated as the weighted average of the expression levels of all probes associated to it.
|
| |
|
| Submission date |
Sep 26, 2013 |
| Last update date |
Jun 17, 2014 |
| Contact name |
Christoph Handschin |
| Organization name |
Biozentrum, University of Basel
|
| Street address |
Spitalstrasse 41
|
| City |
Basel |
| ZIP/Postal code |
4056 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL10740 |
| Series (2) |
| GSE51189 |
Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program [microarray: PGC1a_vs_GFP] |
| GSE51191 |
Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program |
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