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Sample GSM247367 Query DataSets for GSM247367
Status Public on May 22, 2008
Title PPARa-null+0.5% methylcellulose, rep3
Sample type RNA
 
Source name Male adult liver, 129SV background
Organism Mus musculus
Characteristics Samples were collected 24 hrs after the final compound dose.
Treatment protocol Adult male mice were dosed by gavage for 7 consecutive days with either 0, 1, or 3 mg/kg PFOA (ammonium salt) in deionized water; or, 0 or 50 mg/kg Wy14,643 in 0.5% methylcellulose.
Growth protocol none
Extracted molecule total RNA
Extraction protocol Collected tissue was immediately homogenized in TRI reagent and processed on the same day through alcohol precipitation according to the manufacturer's directions. RNA pellets were then washed in cold 80% ethanol and stored at -80 C until further use. Following resuspension in nuclease-free water, the RNA was quantified and evaluated for purity (260nm/280nm ratio) using a NanoDrop ND-1000 spectrophotometer. 100 ug of each sample was then further purified using RNeasy spin columns according to the manufacturer's directions. Approximately 250 ng of each sample was evaluated for quality using an Agilent 2100 Bioanalyzer. RNA samples were used only if they were found to have an RNA Integrity Number of at least 8.5.
Label Digoxigenin-UTP
Label protocol Digoxigenin labeled cRNA was synthesized from 500 ng total RNA using a protocol and labeling kit obtained from the microarray manufacturer which included one round of T7 amplification (Nanoamp RT-IVT labeling kit, Part #4365715, Applied Biosystems).
 
Hybridization protocol Hybridization of target cRNA, labeling controls, and hybridization controls was conducted at 55 C for 16 hrs in a dry shaking incubator using a vendor provided protocol and reagents (Chemiluminescence Detection Kit, Part #4342142, Applied Biosystems)
Scan protocol Microarray images were obtained using an Applied Biosystems 1700 Chemiluminescent Microarray Analyzer and Expression Array System Software version 1.1.1.
Description Adult liver gene expression data from wild-type or PPARa-null mice exposed to either PFOA or Wy14,643
Data processing Data were quantile-normalized and log2 transformed using package ab1700 in Bioconductor
 
Submission date Dec 05, 2007
Last update date May 22, 2008
Contact name Mitchell B Rosen
E-mail(s) rosen.mitch@epa.gov
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 GPL2995
Series (1)
GSE9796 Gene Profiling in the Livers of Wild-Type and PPARalpha-Null Mice Exposed to Perfluorooctanoic Acid (PFOA)

Data table header descriptions
ID_REF Applied Biosystems probe ID
RAW_VALUE Raw signal intensity from expression array system software version 1.1.1.
S/N Signal to noise ratio, system generated metric, s/n>3 is the default for probe detection
FLAG System quantification error code. Data with flag>5000 considered missing.
VALUE same as UNF_VALUE but with flagged values removed
UNF_VALUE NOM_VALUE; log2 transformed, quantile nomalized intensity.

Data table
ID_REF RAW_VALUE S/N FLAG VALUE UNF_VALUE
297784 35303.23 72.56 0 15.39949792 15.39949792
297907 1850.93 11.65 64 11.03920294 11.03920294
297912 5203.68 45.32 0 12.58702778 12.58702778
297935 106.26 -2.62 1 7.111475086 7.111475086
297990 1693.69 6.74 0 10.91468582 10.91468582
297993 93.32 -3.34 131073 6.821411354
298000 17670.17 92.64 0 14.38810314 14.38810314
298038 102.01 -1.3 1 7.047827446 7.047827446
298121 168.95 1.39 0 7.779333182 7.779333182
298130 599.2 1.37 0 9.431871482 9.431871482
298143 7317.42 39.65 0 13.07624897 13.07624897
298150 101.69 -0.51 1 7.04251877 7.04251877
298151 620.84 1.63 0 9.482504092 9.482504092
298155 373.44 3.38 0 8.828814143 8.828814143
298165 871.09 7.45 0 9.949231662 9.949231662
298174 2304.82 14.8 0 11.36991723 11.36991723
298188 144.88 -2.93 1 7.562011166 7.562011166
298200 62796.25 85.16 0 16.24046274 16.24046274
298246 152.57 -2.32 1 7.63705885 7.63705885
298248 125.61 -1.2 1 7.360977458 7.360977458

Total number of rows: 33012

Table truncated, full table size 1466 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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