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Sample GSM586048 Query DataSets for GSM586048
Status Public on Aug 27, 2011
Title casein diet, biological rep4
Sample type RNA
Source name rat liver, casein 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 (20-22ÂșC), 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).
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: -0.55509806535155
upper limit: 2.3961161238099
saturation: 2.885436611132
gamma: 55.3289259732241
sigma: 0.815271055423456
mu: 1.89732997602285
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
Submission date Aug 23, 2010
Last update date Aug 27, 2011
Contact name Tomokazu Konishi
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

Data table header descriptions
VALUE Normalized PM 'Pseudodata' obtained in the pivot output of SuperNORM. (z-scores were also supplied with the pseudo data)
detection call

Data table
ID_REF VALUE detection call z-score
1367452_at 6043.7 P 1.709
1367453_at 3961 P 1.48
1367454_at 3239.7 P 1.372
1367455_at 7252.1 P 1.807
1367456_at 12601.3 P 2.106
1367457_at 1831.4 P 1.063
1367458_at 2069.2 P 1.129
1367459_at 15260.1 P 2.209
1367460_at 4888.1 P 1.594
1367461_at 2030.7 P 1.119
1367462_at 6872.3 P 1.778
1367463_at 7856.8 P 1.85
1367464_at 3239.7 P 1.372
1367465_at 4776.6 P 1.581
1367466_at 3274.3 P 1.377
1367467_at 9406.6 P 1.948
1367468_at 3255.4 P 1.374
1367469_at 13108.5 P 2.127
1367470_at 3996.2 P 1.485
1367471_at 2116.7 P 1.142

Total number of rows: 31099

Table truncated, full table size 798 Kbytes.

Supplementary file Size Download File type/resource
GSM586048.CEL.gz 2.5 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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