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Sample GSM1015550 Query DataSets for GSM1015550
Status Public on Oct 04, 2015
Title SMP30/GNL KO mice rep1
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_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 1.752991023
10338003 1.22837943
10338004 0.922345859
10338017 2.032350754
10338025 0.75662955
10338026 2.017235373
10338029 1.15752713
10338035 0.846937193
10338036 0.992441382
10338037 0.452517752
10338041 1.45598019
10338042 1.154155934
10338044 1.864914872
10338047 0.671477381
10338056 0.261781957
10338059 2.024246446
10338060 0.152332456
10338063 0.570317689
10338064 0.164326638
10338065 0.416882555

Total number of rows: 34760

Table truncated, full table size 669 Kbytes.

Supplementary file Size Download File type/resource
GSM1015550_01_KO-0g_L-2_2.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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