|
| Status |
Public on May 26, 2015 |
| Title |
AMY_8hr_treated_1 |
| Sample type |
RNA |
| |
|
| Source name |
amygdala, ethanol vapor treated, 8 hr
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
gender: male
age: adult (10-12 weeks)
tissue: amygdala
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole brains were cryosectioned at 300um. Specific brain regions were isolated using a 1.25 mm (AMY) or 2.0 mm (NAC, PFC) micropunch. Eight, 6 and 5-8 micropunces were collected from AMY, NAC and PFC, respectively.
Total RNA was isolated using the MagMAX™-96 for Microarrays Total RNA Isolation Kit (Ambion, Austin, TX) using the manufacturer supplied modification to collect both mRNAs and small RNAs. Quality control was performed with the Agilent Tape Station.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNAs were prepared with the Illumina® TotalPrep-96™ RNA Amplification kit from Ambion according to manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
Replicate 1
|
| Data processing |
The R package Lumi was used to transform and normalize the data using variance stabilization transformation and quantile normalization. Only genes with a detection p value ≤ 0.05 and present on ≥ 80% of arrays are included in the normalized data.
Expression value outliers were identified with Grubbs' test and removed.
|
| |
|
| Submission date |
Aug 22, 2014 |
| Last update date |
Jan 04, 2017 |
| Contact name |
Elizabeth Osterndorff-Kahanek |
| Organization name |
University of Texas at Austin
|
| Street address |
2500 Speedway
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE60676 |
Chronic ethanol exposure results in time and brain-region dependent changes in gene coexpression networks. |
|
| Relations |
| Affiliated with |
GSM2407630 |
