|
| Status |
Public on Aug 29, 2013 |
| Title |
BNST/POA Day 60 Male 3 |
| Sample type |
RNA |
| |
|
| Source name |
BNST/POA Day 60 Male 3
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
age: 60 days
tissue: BNST/POA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the BNST/POA using Qiagen AllPrep DNA/RNA Mini Kit (catalog no. 80204).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared by the UCLA Neuroscience Genomics Core.
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
Biological Replicate 2
60MOP3B
|
| Data processing |
Microarray data were processed using the statistical software program R (http://www.r-project.org/) and Bioconductor packages. The raw intensity data were first log2 transformed and then the outlier samples were detected based on the average inter-sample correlations. Three samples with average inter-sample correlations larger than two standard deviations (SDs) from the mean across all samples were removed from follow-up analysis. Then the samples were normalized by quantile normalization. Probes were considered robustly expressed if the detection p value was <0.05 in at least 20 samples (the total number of samples for every genetic/treatment group) in the data set. 57 samples with 13776 probes were retained for differential expression analysis.
|
| |
|
| Submission date |
Aug 19, 2013 |
| Last update date |
Aug 29, 2013 |
| Contact name |
Tuck Cheong Ngun |
| E-mail(s) |
tuckngun@g.ucla.edu
|
| Phone |
310-267-2456
|
| Organization name |
UCLA
|
| Department |
Human Genetics
|
| Lab |
Vilain Lab
|
| Street address |
695 Charles E Young Dr S Gonda 5524
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE49986 |
The organizational effects of testosterone on brain DNA methylome |
|
