|
| Status |
Public on Sep 20, 2016 |
| Title |
HR_Amygdala_P07_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Amygdala, Dissected whole
|
| Organism |
Rattus norvegicus |
| Characteristics |
background strain: Sprague-Dawley
selectively bred line: HR
tissue: brain
brain region: Amygdala
postnatal age: P7
gender: male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Male HR and LR rats (n=5 per phenotype) were sacrificed by rapid decapitation to harvest brain tissue for genome-wide expression profiling. Brains were removed, flash frozen in isopentane cooled to -30°C on dry ice, and then stored at -80°C until further use. Brains were sectioned on a cryostat at -10 to -12°C, and alternating sections of 20 and 300 µm were collected. The 20 µm sections were stained with cresyl violet to identify target anatomical regions in the 300 µm sections. Portions of the amygdala were then dissected and homogenized. RNA was isolated (NucleoSpin RNA II), quantified using a Nanodrop ND-1000 (Wilmington, DE), and stored at -80°C.
|
| Label |
Cy3
|
| Label protocol |
Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit. ds-cDNA labeling with NimbleGen one-color DNA labeling kit.
|
| |
|
| Hybridization protocol |
Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit
|
| Scan protocol |
Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation)
|
| Data processing |
canned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 12.0) for further analysis.
Genes that at least 21 out of 30 samples for Cortex, and genes that at least 10 out 30 samples for Amygdala have values greater than or equal to lower cut-off: 50.0 (“All Targets Value”) were chosen for data analysis.
|
| |
|
| Submission date |
Sep 19, 2016 |
| Last update date |
Sep 20, 2016 |
| Contact name |
Sarah Megan Clinton |
| E-mail(s) |
[email protected]
|
| Organization name |
Virginia Polytechnic Institute and State University
|
| Department |
School of Neuroscience
|
| Street address |
1981 Kraft Dr., Integrated Life Sciences Building 0913
|
| City |
Blacksburg |
| State/province |
Virginia |
| ZIP/Postal code |
24061 |
| Country |
USA |
| |
|
| Platform ID |
GPL19519 |
| Series (1) |
| GSE87082 |
Gene expression within the prefrontal cortex and amygdala in a developing model of high and low anixety and depression-like behavior in rats |
|
