|
| Status |
Public on Oct 07, 2008 |
| Title |
0mg/kg/day PFOA, Rep 1, Block 5 liver (low dose) |
| Sample type |
RNA |
| |
|
| Source name |
Fetal liver, CD-1 background
|
| Organism |
Mus musculus |
| Characteristics |
Pooled litter samples were collected 24 hrs after the final compound dose.
|
| Treatment protocol |
Timed-pregnant CD-1 mice were dosed by oral gavage from gestation day (GD)1 through GD 17 with PFOA (ammonium salt) prepared fresh each day in deionized water. The presence of a sperm plug was considered GD 0. On GD18, dams were euthanized by CO2 asphyxiation and three fetuses per litter were collected for preparation of total RNA from a portion of the liver and lung.
|
| 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 8.0.
|
| Label |
Biotin
|
| Label protocol |
Biotin-labeled cRNA was produced from 2 ug total RNA using an Affymetrix “one-way” labeling kit (cat# 900493).
|
| |
|
| Hybridization protocol |
Following fragmentation, samples were hybridized overnight at 45C according to the protocols recommended by the manufacturer in an Affymetrix Model 640 GeneChip hybridization oven
|
| Scan protocol |
The arrays were washed and stained using an Affymetrix 450 fluidics station as recommended by the manufacturer, and scanned on an Affymetrix Model 3000 scanner.
|
| Description |
Fetal liver gene expression data from full term pups exposed to PFOA throughout gestation.
|
| Data processing |
Probe set data were summarized, background adjusted, and quantile normalized using Robust Multichip Average methodology (Irizarry et al., 2003) as provided by RMA Express (version 0.4).
|
| |
|
| Submission date |
Oct 03, 2008 |
| Last update date |
Aug 28, 2018 |
| 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 |
GPL1261 |
| Series (1) |
| GSE13044 |
Gene expression profiling in the lung and liver of low and high dose Perfluorooctanoic Acid exposed mouse fetuses |
|
| Relations |
| Reanalyzed by |
GSE119085 |
