|
| Status |
Public on Sep 15, 2009 |
| Title |
AD Prefrontal cortex |
| Sample type |
RNA |
| |
|
| Source name |
AD, Prefrontal cortex
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
genotype: WT
gender: Male
age: 8-9 wks
tissue: prefrontal cortex
treatment: AD (ad libitum)
time of sacrifice: day 8
|
| Treatment protocol |
We tested three feeding regimens. One group of mice had ad libitum (AD) access to food, and was used as a control group. The repeated fasting and refeeding (RFR) group of mice were fasted on day 0 and allowed to feed ad libitum on day 1. Amounts of food consumed by the three mice on day 1 were measured. The half amount of food consumed by the RFR mice was given to three mice in another cage for two days (days 0 and 1) (CR group). The fasting followed by refeeding (RFR) and the restriction of food (CR) were repeated up to day 16. Body weights and consumed chow were measured at 20:00 every day, and then the fasting or feeding period was started. In RFR mice, fasting was started on day 0. Four mice of each group were sacrificed at 14:00 under general anesthesia with diethyl ether.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After systemic perfusion with cold phosphate-buffered saline through the heart using a syringe attached to a 21-G needle, whole mouse brains were removed. Coronal sections (1 mm thickness) of mouse brain were prepared on ice. The prefrontal cortex was sliced between 2.5 and 3.5 mm posterior to bregma. Total RNA was immediately prepared from these samples using an RNeasy kit (Qiagen, Hilden, Germany). The quality of purified RNA was assessed by an Agilent 2100 Bioanalyzer using an RNA 6000 Nano Labchip kit (Agilent Technologies, Palo Alto, CA, USA).
|
| Label |
Cy3
|
| Label protocol |
Labeled cRNAs were generated from 400 ng of total RNA using Agilent’s Low RNA Input Linear Amplification Kit (P/N 5188-5339).
|
| |
|
| Hybridization protocol |
Hybridizations were performed using GE Hybridization Kit (P/N 5188-5242) and GE Wash Buffer 1 and 2 (P/N 5188-5325, -5326) as following Agilent's protocol.
|
| Scan protocol |
Microarrays were scanned using Agilent’s DNA Microarray Scanner BA (P/N G2565BA) and data extracted using Agilent's Feature Extraction software, version 9.5 (P/N G2567AA).
|
| Description |
An equal amount of RNA from 4 mice was pooled and used for microarray analysis.
Sample labeling, array processing and scanning, and data extraction were performed as described in One-Color Microarray-Based Gene Expression Analysis – Protocol. These protocols are available for download from Agilent's DNA Microarray Manuals website. The microarrays used were Agilent’s Whole Mouse Genome Oligo Microarrays (P/N G4122F). Probe sequence information is publicly available at Agilent's website.
|
| Data processing |
Data were processed using Agilent’s GeneSpring® GX software, version 7.3 (P/N G1745). Data were transformed by setting all measurements less than 0.01. Data points that did not have detectable signal and those that represent microarray controls were labeled as Absent, those representing either non-uniform or saturated features were labeled as Marginal, and all remaining data points were labeled as Present. All data points were 50 percentile scaled using the 50 percentile of signal intensity value for data points labeled as Present.
The raw data were transformed to log2 by GeneSpring 7.3, and divided with the logarithmic AD value.
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| |
|
| Submission date |
Apr 27, 2009 |
| Last update date |
Sep 16, 2011 |
| Contact name |
Yuta Yamamoto |
| E-mail(s) |
pomme@basic.med.tokushima-u.ac.jp
|
| Phone |
+81-88-633-9004
|
| Fax |
+81-88-633-9008
|
| Organization name |
Institue for Health Biosciences, The University of Tokushima Graduate School
|
| Department |
Stress Science
|
| Street address |
3-18-15 Kuramoto-cho
|
| City |
Tokushima |
| ZIP/Postal code |
770-8503 |
| Country |
Japan |
| |
|
| Platform ID |
GPL4134 |
| Series (1) |
| GSE15860 |
Caloric restriction modified anxiety- and depressive-like behavior and gene expression change in the mouse amygdala |
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