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Sample GSM586050 Query DataSets for GSM586050
Status Public on Aug 27, 2011
Title casein+isoflavone diet, biological rep1
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 (20-22ÂșC), 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: -0.478641739207472
upper limit: 2.19732967583529
saturation: 2.91601914158963
gamma: 59.7605159567935
sigma: 0.804773592008036
mu: 1.8902015126249
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 6016.5 P 1.706
1367453_at 3667.3 P 1.439
1367454_at 3303.6 P 1.382
1367455_at 7499.9 P 1.825
1367456_at 12549.8 P 2.104
1367457_at 1873.5 P 1.076
1367458_at 1963.4 P 1.101
1367459_at 20721.2 uA 2.375
1367460_at 4913.5 P 1.597
1367461_at 2005.2 P 1.112
1367462_at 6912.4 P 1.781
1367463_at 7617.5 P 1.834
1367464_at 2883.7 P 1.309
1367465_at 5166.5 P 1.624
1367466_at 3358.8 P 1.391
1367467_at 10766.3 P 2.021
1367468_at 3260.6 P 1.375
1367469_at 12475.9 P 2.1
1367470_at 4470 P 1.546
1367471_at 2228.2 P 1.169

Total number of rows: 31099

Table truncated, full table size 799 Kbytes.

Supplementary file Size Download File type/resource
GSM586050.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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