gender: male strain: C57BL/6J tissue: liver diet: Western diet for 20 weeks
Treatment protocol
The mice were divided into 10 groups of 6 mice each, housed in groups of 3 per cage and fed one of the following diets for 20 weeks : AIN93G (control), AIN93G containing 0.05% quercetin (0.05% quercetin, (Funakoshi, Tokyo, Japan)), a high fat, high cholesterol and high sucrose Western-style diet (39.9% of energy from fat (20% unsalted butter, 1% soy oil, 0.15% cholesterol) and 34.0% of energy from sucrose) (Oriental Yeast) or this Western diet supplemented with 0.05% quercetin.
Growth protocol
Five-week-old male C57BL/6J mice were obtained from the Institute for Animal Reproduction, Charles River Japan Inc. (Ibaraki, Japan). The mice were housed under conditions of 24± 1°C, 55 ± 5% humidity, and 12 hour light/dark photocycles (dark period from 0800 to 2000) with free access to water and a standard nonpurified diet (NMF, Oriental Yeast Co., Tokyo, Japan) for a week prior to the experiment.
Extracted molecule
total RNA
Extraction protocol
The mice were killed under anesthesia with pentobarbital, and blood and liver tissue were immediately collected. Total RNA was extracted from liver tissues using an RNeasy Midi Kit (Qiagen KK, Tokyo, Japan) according to the manufacturer’s instructions.
Label
biotin
Label protocol
Double-stranded cDNA was synthesized from the total RNA of each mouse using the One-Cycle cDNA Synthesis Kit (Affymetrix Japan KK, Tokyo, Japan) with a T7-(dT)24 primer. Biotin-labeled cRNA was then synthesized using an IVT Labeling Kit (Affymetrix). The biotin-labeled cRNA was further purified and fragmented using the Sample Cleanup Module (Affymetrix).
Hybridization protocol
Fragmented cRNA were hybridized to an array (Mouse Genome 430 2.0 array, Affymetrix) at 45°C for 16 h.
Scan protocol
After hybridization, the gene chips were washed and stained using a GeneChip Fluidics Station 450 (Affymetrix) and then scanned (GeneChip Scanner; Affymetrix) with the GeneChip Operation Software Ver. 1.4 (Affymetrix).
Description
Gene expression data from liver after 20 week feeding of western diet
Data processing
Data analysis was performed with a GeneChip Operating Software (Ver. 1.4) using Affymetrix default analysis settings and global scaling as normalization method..