strain background: C57BL/6NCrSlc (Ishigami, A., Am. J. Pathol., 2002) gender: male genotype/variation: wild type tissue: liver diet: Vitamin C (VC)-deprived
Treatment protocol
The concentration of AA in the drinking water was enough to maintain normal AA levels in all tissues. EDTA was added to stabilize AA in drinking water, which retained that stable state for at least for 4 days. Water bottles were changed every 3 or 4 days. Other than the water, all mice were fed an AA-deficient diet (CL-2, CLEA Japan, Tokyo, Japan) ad libitum.
Growth protocol
WT mice were fed a VC-deprived diet and had free access to water without VC. Animals were maintained on a 12-h light/dark cycle in a controlled environment.
Extracted molecule
total RNA
Extraction protocol
Total RNA was extracted by using ISOGEN® (Wako Pure Chemical, Osaka, Japan). Briefly, liver was homogenized with a teflon-pestle homogenizer in ISOGEN, and total RNA was extracted according to the manufacturer’s protocol.
Label
biotin
Label protocol
GeneChip® WT Terminal Labeling Kit (Affymetrix), performed by Genetic Lab Inc., Sapporo, Japan
Hybridization protocol
GeneChip® Hybridization Oven 640 (Affymetrix)
Scan protocol
GeneChip® Scanner 3000 7G (Affymetrix)
Description
Wild_2
Data processing
The perfect match data were normalized by using the SuperNORM data service (Skylight Biotech Inc., Akita, Japan) according to a three-parameter lognormal distribution model [details on PMID 18764774, 18958174, 22784577]. The log values are log10 (rawdata - gamma): z-score = (log10 (rawdata- gamma) - mu)/sigma.
