|
| Status |
Public on Jul 28, 2007 |
| Title |
amygdala rattus_norvegicus_strain iNP animal_number 12 |
| Sample type |
RNA |
| |
|
| Source name |
rattus_norvegicus_strain_iNP-1_adult_male
|
| Organism |
Rattus norvegicus |
| Characteristics |
Genotype: Strain iNP
_Age_90-100 days old
_Alcohol_naive
|
| Treatment protocol |
Animal was sacrificed by decapitation between 0900 and 1000 hr. The head was immediately placed in a cold box maintained at -15ºC, where the brain was rapidly removed and placed on a glass plate for dissection. All equipment used to obtain tissue was treated with RNAse Zap.
|
| Growth protocol |
Animals were received in our facilities 3 weeks prior to the experiment. Rats were double housed on a 12:12 light dark cycle with lights on at 0700 hours. Rats had water and rat chow ad libitum. Animals were habituated (by the same experimenter) to handling and to the guillotine daily between 0900 - 1000 hr for 10 days prior to sacrifice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
RNA from each individual rat was labeled and analyzed separately. Starting with 10 µg of total RNA, first and second-strand cDNA synthesis was carried out according to the standard protocol. Biotinylated cRNA was synthesized in vitro from the double-stranded cDNA using the ENZO BioArray High Yield RNA Transcript Labeling Kit according to the Affymetrix protocol.
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| |
|
| Hybridization protocol |
Fifteen µg of fragmented, biotinylated cRNA was mixed into 300 µl of hybridization cocktail, of which 200 µl was used for each hybridization. Hybridization was for 17 hr at 42°C. Washing, staining and scanning were carried out according to the standard protocol.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
Gene expression data from brain of adult rats
|
| Data processing |
The data were analyzed with BioConductor package 'affy', function mas5 using using default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.
|
| |
|
| Submission date |
Mar 17, 2006 |
| Last update date |
Mar 20, 2013 |
| Contact name |
Mark William Kimpel |
| E-mail(s) |
[email protected]
|
| Organization name |
Indiana University
|
| Department |
Psychiatry
|
| Lab |
W.J. McBride
|
| Street address |
15032 Hunter Court
|
| City |
Westfield |
| State/province |
IN |
| ZIP/Postal code |
46074 |
| Country |
USA |
| |
|
| Platform ID |
GPL85 |
| Series (1) |
| GSE4494 |
Functional Gene Expression Differences between Inbred Alcohol-Preferring (iP) and non-preferring (iNP) Rats |
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