|
| Status |
Public on Oct 04, 2015 |
| Title |
SMP30/GNL KO mice rep2 |
| Sample type |
RNA |
| |
|
| Source name |
SMP30/GNL KO_AA-deficient
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6NCrSlc (Ishigami, A., Am. J. Pathol., 2002)
gender: male
genotype/variation: SMP30/GNL KO
tissue: liver
diet: ascorbic acid (AA)-deficient
|
| 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 |
KO_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.
|
| |
|
| Submission date |
Oct 05, 2012 |
| Last update date |
Oct 04, 2015 |
| Contact name |
Tomokazu Konishi |
| E-mail(s) |
konishi@akita-pu.ac.jp
|
| 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 |
GPL6246 |
| Series (1) |
| GSE41365 |
Influence of ascorbic acid depletion on gene expression in liver and lipid metabolism |
|
