|
| Status |
Public on Jan 14, 2011 |
| Title |
OPMD Sample_O6 |
| Sample type |
RNA |
| |
|
| Source name |
Quadricept
|
| Organism |
Mus musculus |
| Characteristics |
background strain: FvB
genotype/variation: OPMD
gender: Male
age: 6 week-old
|
| Growth protocol |
A17.1 transgenic mice have previously been described. Male A17.1 mice and WT controls were generated by crossing the heterozygous carrier strain A17.1 obtained from Rubinsztein's group with the FvB background mice. The mice were genotyped by PCR 3–4 weeks after birth. Wild type FvB and A17.1 mice were housed in minimal disease facilities (Royal Holloway, University of London) with food and water ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from skeletal muscles using RNA Bee (Amsbio) according to the manufacturer's instructions. RNA integration number (RIN) was determined with RNA 6000 Nano (Agilent Technologies). RNA with RIN >7 were used for subsequent steps.
|
| Label |
biotin
|
| Label protocol |
RNA labelling was performed with the Illumina® TotalPrep RNA Amplification kit (Ambion) according to the manufacturer's protocol, and subsequently was hybridized to Illumina Mouse v1.1 Bead arrays.
|
| |
|
| Hybridization protocol |
According to Illumina protocols
|
| Scan protocol |
According to Illumina protocols
|
| Description |
1870382054_E
|
| Data processing |
Before data analysis, microarray measurements were normalized to remove systematic errors by balancing the fluorescence intensities using the quantile method. Each time point has been normalized separately. Next, PCA plots were generated to assess the quality of the data. This analysis showed that 47% of the variations within each data set were attributed to the genetic variation between the WT and the transgenic mice. Subsequently, statistical analysis was conducted using limma package in R to identify genes with significant differences in expression pattern between A17.1 and WT. Statistical analysis includes a cut-off P-value of 0.05 and FDR correction provided in the limma package in R. Probe annotation was made with the Illumina mouse whole-genome bead array version 1 annotation package.
|
| |
|
| Submission date |
Jan 13, 2011 |
| Last update date |
Jan 14, 2011 |
| Contact name |
Seyed Yahya Anvar |
| E-mail(s) |
s.y.anvar@lumc.nl
|
| Phone |
0031715269489
|
| Organization name |
Leiden University Medical Center
|
| Department |
Center for Human and Clinical Genetics
|
| Street address |
Einthovenweg 20
|
| City |
Leiden |
| ZIP/Postal code |
2300RC |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL6481 |
| Series (1) |
| GSE26604 |
Molecular and phenotypic characterization of a mouse model of oculopharyngeal muscular dystrophy reveals severe muscular atrophy restricted to fast glycolytic fibres |
|
