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| Status |
Public on Aug 27, 2011 |
| Title |
casein+isoflavone diet, biological rep5 |
| Sample type |
RNA |
| |
|
| Source name |
rat liver, casein+isoflavone diet fed for 14 days
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
sex: male
tissue: liver
|
| Treatment protocol |
Each group was fed a diet containing 200 g/kg of protein in the form of casein, soy protein, or freeze-dried tofu. The experimental diets were as follows: 1) casein diet (C); 2) C containing isoflavone (CI); 3) soy protein diet (S); 4) S containing isoflavone (SI); 5) a diet containing 100 g/kg each of protein derived from casein and freeze-dried tofu (T10); and 6) a diet containing 200 g/kg of protein derived from freeze-dried tofu (T20) (Table 1). CI and SI were supplemented with a mixture of isoflavones to match the isoflavone level of T20.
|
| Growth protocol |
Male Sprague-Dawley rats were obtained from Charles River Japan (Kanagawa, Japan) at 4 week of age. Animals were housed individually in a room with a controlled temperature (20-22ºC), humidity (55-65%), and 12-h-light/-dark cycle. During their adaptation to the conditions, rats were fed a commercial non-purified diet (Type NMF; Oriental Yeast Co., Tokyo, Japan) for 5 days. Rats were allowed free access to diet and water.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At the end of the experimental period, the animals were sacrificed by bleeding from the abdominal aorta under diethyl ether anesthesia, and the liver was quickly excised. Hepatic total RNA was extracted and purified using the RNeasy Mini Kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
Ten micrograms of total RNA was processed to prepare biotinylated cRNA using One-Cycle Target Labeling and Control Reagents (Afflymetrix).
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| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C, according to the manual supplied by Affymetrix (P/N 702232 Rev. 2). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned with a GCS 3000 scanner (GCOS V1.2, Affymetrix).
|
| Description |
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.362716655680217
upper limit: 2.42117340643909
saturation: 2.92865336567959
gamma: 51.529121802478
sigma: 0.814115956879256
mu: 1.84512227913562
|
| Data processing |
The data were analyzed by using SuperNORM (V 1.7, Skylight Biotech Inc.) accoring to a parametric method (Konishi, T., 2008, Stat Appl Genet Mol Biol 7: Article 25.). A row of the data table presents z-scores of the PM data of a gene, in accordance with the order of the Cell appears in the CDF file. The PM data are further summarized to find z-scores and pseudo data value of a gene. The signal intensity represents the pseudo data, of which center of intensity for each array was arbitrarily set to 256. For details of the methodology, visit http://www.super-norm.com/eng/index.html.
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| |
|
| Submission date |
Aug 23, 2010 |
| Last update date |
Aug 27, 2011 |
| Contact name |
Tomokazu Konishi |
| E-mail(s) |
konishi@akita-pu.ac.jp
|
| Phone |
+81-18-872-1603
|
| Organization name |
Akita Prefectural University
|
| Department |
Bioresource Sciences
|
| Lab |
Molecular Genetics
|
| Street address |
Shimoshinjyo Nishi
|
| City |
Akita |
| State/province |
Akita |
| ZIP/Postal code |
010-0195 |
| Country |
Japan |
| |
|
| Platform ID |
GPL1355 |
| Series (1) |
| GSE23748 |
Tofu decreases serum lipid levels and modulates hepatic gene expression involved in lipid metabolism in rats |
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