NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1015552 Query DataSets for GSM1015552
Status Public on Oct 04, 2015
Title SMP30/GNL KO mice, AA supplemented rep1
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_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
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

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

Data table
ID_REF VALUE
10338001 1.740950683
10338003 1.241982978
10338004 0.965303122
10338017 2.002248312
10338025 0.796446579
10338026 1.973607527
10338029 1.182141341
10338035 0.875308454
10338036 1.039277943
10338037 0.488710945
10338041 1.468251467
10338042 1.180120099
10338044 1.804077887
10338047 0.765673224
10338056 0.194114916
10338059 2.000750577
10338060 0.143903635
10338063 0.623153572
10338064 0.366125238
10338065 0.557902538

Total number of rows: 34760

Table truncated, full table size 669 Kbytes.




Supplementary file Size Download File type/resource
GSM1015552_03_KO-1.5g_L-2_7.CEL.gz 4.0 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap