|
| Status |
Public on Feb 05, 2009 |
| Title |
AKR/J_Amygdala 251197818009 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
AKR/J_Amygdala
|
| Organism |
Mus musculus |
| Characteristics |
Age 6-8 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol followed by Qiagen Rneasy Cleanup
|
| Label |
Cy3
|
| Label protocol |
Agilent Direct Label kit (15ug total RNA input)
|
| |
|
| Channel 2 |
| Source name |
Stratagene Mouse Universal Reference RNA
|
| Organism |
Mus musculus |
| Characteristics |
Stratagene Mouse Universal Reference RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol followed by Qiagen Rneasy Cleanup
|
| Label |
Cy5
|
| Label protocol |
Agilent Direct Label kit (15ug total RNA input)
|
| |
|
| |
| Hybridization protocol |
Agilent Hyb. Protocol
|
| Scan protocol |
Agilent Scanner
|
| Description |
251197818009
|
| Data processing |
The original arrays consist of a total of 22393 transcripts. Data were normalized by the lowess function using the Statistical microarray analysis (SMA) package in R (http://stat-www.berkeley.edu/users/terry/zarray/Software/smacode.html), and further scale normalized. Raw data from Nadler et al. (2006) with the addition of another ten strains were normalized as a single dataset. The log-ratio of background-subtracted Cy3 signal to background-subtracted Cy5 signal was calculated for each spot, and used for subsequent analyses. 20868 transcripts remained after the control genes were removed and the 50 probesets spotted 10 times on the array were averaged. Since the array data was collected over period of two years, we investigated the possibility of a calendar time effect. We performed principal component analysis (PCA) on all arrays and the first two PCs were plotted against time. A significant time effect was noted in the data. To correct for this effect, arrays were divided into 5 equally sized groups (shown in color), and an ANOVA model applied to each gene with the “defined” time group as a covariate. The residuals from the ANOVA model were treated as the final expression values and used in all the subsequent analyses. PCA analysis on the new adjusted expression indicated this procedure removed the time effect efficiently.
|
| |
|
| Submission date |
Feb 06, 2008 |
| Last update date |
Feb 06, 2008 |
| Contact name |
Hanwen Huang |
| Organization name |
UNC
|
| Street address |
University of North Carolina
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL6466 |
| Series (1) |
| GSE10415 |
7 Brain Regions in 20 Inbred Strains of Laboratory Mice |
|
