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Sample GSM1015554 Query DataSets for GSM1015554
Status Public on Oct 04, 2015
Title Wild type rep1
Sample type RNA
Source name Wild type_VC-deprived
Organism Mus musculus
Characteristics 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_1
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
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

Data table header descriptions
VALUE parametric: z-score of logarithms

Data table
10338001 1.761932454
10338003 1.247335461
10338004 0.936102054
10338017 2.01672087
10338025 0.760795495
10338026 2.023949506
10338029 1.173282441
10338035 0.863134306
10338036 0.99890798
10338037 0.582366532
10338041 1.4260572
10338042 1.141889578
10338044 1.85393449
10338047 0.910257891
10338056 0.326270147
10338059 2.023888577
10338060 0.306164183
10338063 0.73196409
10338064 0.474948862
10338065 0.702820088

Total number of rows: 34760

Table truncated, full table size 669 Kbytes.

Supplementary file Size Download File type/resource
GSM1015554_05_WT-0g_L-2_12.CEL.gz 4.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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