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Sample GSM326976 Query DataSets for GSM326976
Status Public on Oct 07, 2008
Title 0mg/kg/day PFOA, Rep 2, Block 1 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

Data table header descriptions
ID_REF Affymetrix probe set ID
VALUE RMA summarized, Log2 transformed, quantile nomalized intensity.

Data table
ID_REF VALUE
1415670_at 7.747689
1415671_at 8.400688
1415672_at 9.069872
1415673_at 6.969074
1415674_a_at 7.330165
1415675_at 6.453883
1415676_a_at 9.106261
1415677_at 7.602966
1415678_at 8.435003
1415679_at 9.228071
1415680_at 7.684062
1415681_at 8.138042
1415682_at 8.621079
1415683_at 8.787685
1415684_at 6.30068
1415685_at 7.238622
1415686_at 7.835285
1415687_a_at 9.339801
1415688_at 8.482231
1415689_s_at 6.588234

Total number of rows: 45037

Table truncated, full table size 893 Kbytes.




Supplementary file Size Download File type/resource
GSM326976.CEL.gz 3.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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