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Sample GSM247366 Query DataSets for GSM247366
Status Public on May 22, 2008
Title wild-type+0mg/kg PFOA, 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 27230.48 46.6 0 14.98963914 14.98963914
297907 245.09 0.39 1 7.998641569 7.998641569
297912 5580.86 42.56 0 12.64029507 12.64029507
297935 158.19 0.32 1 7.368822799 7.368822799
297990 2497.49 6.24 0 11.41661365 11.41661365
297993 159.66 -1.66 1 7.380381924 7.380381924
298000 16648.28 58.33 0 14.26686407 14.26686407
298038 171.95 0.33 1 7.486589795 7.486589795
298121 233.54 -0.81 1 7.929322096 7.929322096
298130 1683.85 2.18 0 10.80699977 10.80699977
298143 4576.79 13.69 0 12.34012968 12.34012968
298150 110.76 0.57 1 6.865089445 6.865089445
298151 488.75 -0.66 1 8.99615391 8.99615391
298155 256.9 1.3 0 8.069993367 8.069993367
298165 1043.06 12.19 0 10.07648155 10.07648155
298174 1787.46 12.35 0 10.89412074 10.89412074
298188 157.33 -0.42 1 7.360793727 7.360793727
298200 65935.61 67.21 0 16.28859483 16.28859483
298246 241.91 -0.86 1 7.979648875 7.979648875
298248 40.57 -5.31 131073 6.744864181

Total number of rows: 33012

Table truncated, full table size 1469 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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