|
| Status |
Public on May 22, 2008 |
| Title |
PPARa-null+3mg/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. |
