|
| Status |
Public on Aug 24, 2014 |
| Title |
Ethanol-treated A28 |
| Sample type |
RNA |
| |
|
| Source name |
treated mouse
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J x FVB/NJ F1
tissue: frontal cortex
stress: ethanol
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Ambion's mirVana™ miRNA Isolation Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the Illumina® TotalPrep RNA Amplification Kit
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
5665159054_A
treated mouse
|
| Data processing |
The data were normalized using quantile normalization with lumi package in R
The quality of the Illumina bead summary data was assessed using the Bioconductor packages Lumi and arrayQualityMetrics. Data preprocessing included variance stabilization and quantile normalization using the Lumi package. Statistical analysis comparing ethanol-treated and control groups was performed using the Bioconductor package limma, which implements an empirical Bayes approach in R (Smyth 2005). False discovery rate (FDR) was assessed using the Benjamini-Hochberg method.
|
| |
|
| Submission date |
Aug 29, 2013 |
| Last update date |
Aug 24, 2014 |
| Contact name |
Yury O. Nunez |
| E-mail(s) |
nunezyo@gmail.com
|
| Phone |
210-567-8094
|
| Organization name |
University of Texas at Austin
|
| Department |
Pharmacy
|
| Lab |
Pharmacogenomics
|
| Street address |
7703 Floyd Curl Drive MC6220
|
| City |
San Antonio |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE50427 |
Gene (mRNA) expression profiling in frontal cortex of ethanol-treated mice |
|
