GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM586068 Query DataSets for GSM586068
Status Public on Aug 27, 2011
Title casein + tofu diet, biological rep4
Sample type RNA
Source name rat liver, casein + tofu 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: -0.493933004436287
upper limit: 2.85485408067437
saturation: 3.43592215936937
gamma: 49.1723479621268
sigma: 0.782537444825238
mu: 1.86271311333722
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 6155.5 P 1.719
1367453_at 3899.1 P 1.472
1367454_at 3602.1 P 1.429
1367455_at 6837.9 P 1.775
1367456_at 13706.2 P 2.151
1367457_at 1701.3 P 1.024
1367458_at 1970.4 P 1.103
1367459_at 16242.4 P 2.243
1367460_at 5182.5 P 1.626
1367461_at 1948.1 P 1.097
1367462_at 6483.6 P 1.747
1367463_at 8581.2 P 1.898
1367464_at 3017.4 P 1.333
1367465_at 5591.4 P 1.667
1367466_at 3351.5 P 1.39
1367467_at 10524.8 P 2.008
1367468_at 3043.2 P 1.338
1367469_at 11524.8 P 2.057
1367470_at 3670.7 P 1.439
1367471_at 2386.5 P 1.206

Total number of rows: 31099

Table truncated, full table size 799 Kbytes.

Supplementary file Size Download File type/resource
GSM586068.CEL.gz 2.5 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap