|
| Status |
Public on Aug 28, 2010 |
| Title |
Mouse cortex of control mice, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
littermate controls
|
| Organism |
Mus musculus |
| Characteristics |
genetic background: C57BL/6
tissue: adult forebrain cortex
genotype: CamKII-Cre/+;Dicer flox/+ or +/+;Dicer flox/flox
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mouse mutant phenotypes were identified by genotyping as wild-type or mutants. All brain samples were dissected and snap frozen in liquid N2. All samples were prepared using the miRVana PARIS kit (Ambion). Total RNA (200 ng per sample) was labeled using the Affymetrix GeneChip WT cDNA Synthesis and Amplification Kit (Ambion).
|
| Label |
biotin
|
| Label protocol |
Total RNA (200 ng per sample) was labeled using the Affymetrix GeneChip® WT cDNA Synthesis and Amplification Kit protocol and hybridized to the arrays as described by the manufacturer (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
The cRNA hybridization cocktail was incubated overnight at 45°C while rotating in a hybridization oven. After 16 hours of hybridization, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip fluidics station 450, according to the Affymetrix-recommended protocol
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Description |
n/a
|
| Data processing |
The background subtraction and normalization of probe set intensities was performed using the method of Robust Multiarray Analysis (RMA) described by Irizarry et al. (Irizarry et al., 2003). To identify differentially expressed genes, gene expression intensity was compared using a moderated t-test and a Bayes smoothing approach developed for a low number of replicates (Smyth, 2004). To correct for the effect of multiple testing, the false discovery rate, was estimated from p values derived from the moderated t-test statistics (Benjamini et al., 2001). The analysis was performed using the affylmGUI Graphical User Interface for the Limma microarray package.
MoGene-1_0-st-v1.r3.pgf
MoGene-1_0-st-v1.r3.mps
|
| |
|
| Submission date |
Aug 27, 2010 |
| Last update date |
Aug 27, 2010 |
| Contact name |
Ezequiel L Calvo |
| E-mail(s) |
[email protected]
|
| Organization name |
CRCHUL
|
| Department |
Molecular Endocrinilogy
|
| Lab |
Microarrays
|
| Street address |
2705 Boul. Laurier
|
| City |
Quebec |
| State/province |
Quebec |
| ZIP/Postal code |
G1V 4G2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE23847 |
Genetic ablation of Dicer in adult forebrain neurons results in abnormal tau hyperphosphorylation and neurodegeneration |
|
