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Sample GSM565110 Query DataSets for GSM565110
Status Public on Oct 01, 2010
Title PPARalpha-null mouse + 0mg/kg PFOS, biological rep5
Sample type RNA
 
Source name PPARalpha-null, liver, left lobe, 0mg/kg PFOS, 7 day exposure
Organism Mus musculus
Characteristics strain: 129S4/SvJae-Pparatm1Gonz/J
genotype: PPARalpha-null
tissue: liver
gender: male
age: 6-9 months
treatment: untreated
treatment dosage: 0mg/kg
treatment time: 7 days
Treatment protocol PPARα-null and wild-type male mice at 6-9 months of age were dosed by gavage for 7 consecutive days with either 0, 3, or 10 mg/kg PFOS (potassium salt) in 0.5% Tween 20.
Growth protocol Animals were housed 5 per cage and allowed to acclimate for a period of one week prior to the conduct of the study. Food and municipal tap water were provided ad libitum. Animal facilities were controlled for temperature (20-24°C), relative humidity (40-60%), and kept under a 12 hr light-dark cycle.
Extracted molecule total RNA
Extraction protocol Collected tissue (≤ 50 mg) was immediately placed in 1 ml RNAlater and stored at -20◦C. RNA preparations were then completed by homogenizing the tissue in 1 ml TRI reagent followed by processing according to the manufacturer’s instructions.
Label Biotin
Label protocol Biotin-labeled cRNA was produced from 5 ug total RNA using Enzo Single-Round RNA Amplification and Biotin Labeling System (Cat. No. 42420-10, Enzo Life Sciences Inc, Farmingdale, NY).
 
Hybridization protocol Following fragmentation, samples were hybridized overnight at 45oC in an Affymetrix Model 640 GeneChip hybridization oven.
Scan protocol Arrays were washed and stained using an Affymetrix 450 fluidics station, and scanned on an Affymetrix Model 3000 scanner.
Description Null_0mg/kg-5

Liver gene expression data from control PPARalpa-null mice.
Data processing Microarray data were summarized, background adjusted, and quantile normalized using Robust Multichip Average methodology (RMA Express, ver. 1.0). Prior to statistical analysis, microarray data were filtered to remove probe sets with weak or no signal. Data were analyzed for each strain using a one-way ANOVA across dose (Proc GLM, SAS ver. 9.1, Cary, NC). Individual treatment contrasts were evaluated using a pairwise t-test of the least square means.
 
Submission date Jul 09, 2010
Last update date Oct 01, 2010
Contact name Mitchell B Rosen
E-mail(s) [email protected]
Phone 919-541-2223
Fax 919-541-4017
Organization name U.S. EPA
Department Reproductive Toxicology
Lab GEEBB
Street address 2525 Hwy 54
City Research Triangle Park
State/province NC
ZIP/Postal code 27711
Country USA
 
Platform ID GPL1261
Series (1)
GSE22871 Expression data from wild-type and PPARalpha-null mice exposed to perfluorooctane sulfonate (PFOS)

Data table header descriptions
ID_REF
VALUE RMA summarized, log2 transformed, quantile-nomalized intensity

Data table
ID_REF VALUE
1415670_at 8.872098
1415671_at 10.653829
1415672_at 11.072407
1415673_at 7.1872
1415674_a_at 8.377379
1415675_at 8.076101
1415676_a_at 11.800364
1415677_at 11.535576
1415678_at 11.185068
1415679_at 11.505503
1415680_at 8.762365
1415681_at 10.324219
1415682_at 8.363389
1415683_at 10.840307
1415684_at 10.034132
1415685_at 9.020654
1415686_at 10.43125
1415687_a_at 11.599839
1415688_at 10.689968
1415689_s_at 9.628328

Total number of rows: 45101

Table truncated, full table size 897 Kbytes.




Supplementary file Size Download File type/resource
GSM565110.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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