|
| Status |
Public on Apr 15, 2016 |
| Title |
CIE mouse, BNST, sacrificed at 7 days, biological replicate 59 |
| Sample type |
RNA |
| |
|
| Source name |
BNST brain dissection, ethanol inhalation chamber, tissue harvested 7 days after final inhalation chamber session
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: brain, bed nucleus of the stria terminalis
sacrifice time: 7 days post final vapor chamber session
Sex: male
|
| Treatment protocol |
Adult male C57BL/6J mice were divided into two groups of 24. One group (CIE) received ethanol vapor exposure for 16 hours/day for 4 days while the other group was similarly handled but received only air exposure. For CIE mice, ethanol was volatized by passing air through an air stone submerged in 95% ethanol. Chamber ethanol concentrations were monitored daily and air flow was adjusted to maintain ethanol concentrations within a range (10-13 mg/l air). Before each chronic ethanol exposure cycle, intoxication was initiated in the CIE group by administration of ethanol (1.6 g/kg), and blood ethanol concentration was stabilized by injection of the alcohol dehydrogenase inhibitor pyrazole (1 mmol/kg). Both ethanol and pyrazole were administered intraperitoneally (i.p.) in a volume of 0.02 ml/g body weight. Ctrl mice were handled similarly, but administered saline and pyrazole (i.p.) prior to being placed in control chambers that delivered only air. Following 4 days in the inhalation chamber, mice underwent 7 days of complete abstinence from ethanol. At the end of the abstinence period, mice were returned to the inhalation chamber to begin the next cycle of CIE. This pattern of 4 days CIE (or control air) exposure followed by 7 days abstinence was repeated for four complete cycles.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue from individual mice was homogenized using a Tekmar homogenizer, and total RNA was isolated with reagents and procedures provided by the RNeasy Mini Kit (Qiagen, Valencia, CA, USA).
|
| Label |
biotin
|
| Label protocol |
Botinylated cRNA samples were prepared according to Affymetrix protocols.
|
| |
|
| Hybridization protocol |
Following fragmentation, cRNA samples were hybridized for 16 hr to GeneChip Mouse Genome 430 2.0 arrays by procedures outlined by Affymetrix.
|
| Scan protocol |
Arrays were washed, stained with streptavidin-phycoerythrin and scanned using the Affymetrix GeneChip Scanner 3000.
|
| Data processing |
Microarrays were separated by RNA hybridization batch for initial normalization. Each batch was background corrected with the Robust Multi-array Average (RMA) technique and normalized by quantile normalization. The second step involved subjecting all microarrays together to another round of quantile normalization. Finally, ComBat with hybridization group as the batch effect was used to remove any remaining batch effects reflected in the data. Network analysis with WGCNA and bioinformatics analysis were used to identify modules of co-expressed genes representing specific biological pathways. Modules were overlapped with genes differentially expressed between CIE and Ctrl mice at each time-point to identify modules regulated at specific times after CIE.
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| |
|
| Submission date |
Aug 28, 2015 |
| Last update date |
Apr 15, 2016 |
| Contact name |
Michael Miles |
| E-mail(s) |
Michael.Miles@vcuhealth.org
|
| Organization name |
Virginia Commonwealth Univ.
|
| Department |
Pharmacology and Toxicology
|
| Lab |
Miles
|
| Street address |
PO Box 980613
|
| City |
Richmond |
| State/province |
VA |
| ZIP/Postal code |
23298 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (2) |
| GSE72516 |
Chronic Intermittent Ethanol by vapor chamber gene expression time-course in basal nucleus of the stria terminalis [BNST] |
| GSE72517 |
Chronic Intermittent Ethanol by vapor chamber gene expression time-course in five brain regions |
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