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Sample GSM1015553 Query DataSets for GSM1015553
Status Public on Oct 04, 2015
Title SMP30/GNL KO mice, AA supplemented rep2
Sample type RNA
Source name SMP30/GNL KO_AA suplemented
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)-supplemented
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+AA_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
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 1.825124566
10338003 1.261648818
10338004 0.906437358
10338017 2.069353313
10338025 0.725861315
10338026 2.067720287
10338029 1.143680538
10338035 0.85260421
10338036 0.969402348
10338037 0.49103279
10338041 1.410900767
10338042 1.139217296
10338044 1.881879873
10338047 0.698099209
10338056 0.299681733
10338059 2.131487453
10338060 0.161713606
10338063 0.60909795
10338064 0.227380943
10338065 0.446264545

Total number of rows: 34760

Table truncated, full table size 668 Kbytes.

Supplementary file Size Download File type/resource
GSM1015553_04_KO-1.5g_L-4_9.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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