|
| Status |
Public on Sep 23, 2011 |
| Title |
SAM/R-1 + CCH_4 |
| Sample type |
RNA |
| |
|
| Source name |
hippocampus, SAM/R-1, CCH, reprecate4
|
| Organism |
Mus musculus |
| Characteristics |
background strain: AKR/J
tissue: hippocampus
age: 8-week-old
gender: male
genotype/variation: SAM/R-1
diet: CCH
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the tissues by using the RNeasy Lipid Tissue Mini Kit (Qiagen, Valencia, CA). RNA was treated with DNase 1 (Qiagen) and cleaned using the RNeasy Mini Kit (Qiagen). The purity and integrity of the isolated total RNA were analyzed by ultraviolet spectrophotometry and an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA). All RNA samples exhibited a 260/280 ratio between 2.0 and 2.2, and a 28S:18S ratio of >1.6; the RNA integrity number (RIN) was >9.0.
|
| Label |
Cy3
|
| Label protocol |
Five hundred ng of the RNA sample was transcribed using oligo(dT)-based T7 promoter primer and MMLV-RT in the first- and second-strand cDNA synthesis reactions. The double-stranded cDNAs were used as templates in the preparation of fluorescent complementary RNAs (cRNAs) in the presence of T7 RNA polymerase and cyanine 3-CTP dye in an in vitro transcription reaction.
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| |
|
| Hybridization protocol |
The labeled cRNAs were purified, fragmented, and hybridized to microarrays in a rotating hybridization oven at 10 rpm for 17 h at 65 °C.
|
| Scan protocol |
After hybridization, the microarrays were washed according to the manufacturer’s protocol and scanned on an Agilent DNA Microarray Scanner with the Scan Control software (Agilent Technologies).
|
| Description |
The mouse model we used in our experiment (the senescence-accelerated mouse (SAM)) was established through phenotypic selection from a common genetic pool of AKR/J strain of mice.
Gene expression of SAM/R-1 with CCH feeding
|
| Data processing |
The resulting images were processed, and raw data were collected using Agilent’s Feature Extraction software. The gene expression data were analyzed using GeneSpring GX 10 (Agilent). The signal intensity for each probe was normalized by a percentile shift, in which each measurement was divided by the 75th percentile of all measurements in its array.
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| |
|
| Submission date |
Aug 23, 2011 |
| Last update date |
Sep 24, 2011 |
| Contact name |
Toshio Kojima |
| Organization name |
Toyohashi University of Technology
|
| Department |
Health Care Center
|
| Street address |
1-1 Hibarigaoka Tenpaku-cho
|
| City |
Toyohashi |
| ZIP/Postal code |
441-8580 |
| Country |
Japan |
| |
|
| Platform ID |
GPL7202 |
| Series (1) |
| GSE31606 |
Hippocampal gene network analysis to determine the effects of coral calcium hydride in an experimental model of accelerated senescence |
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