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Sample GSM326986 Query DataSets for GSM326986
Status Public on Oct 07, 2008
Title 1mg/kg/day PFOA, Rep 2, Block 3, lung (low dose)
Sample type RNA
 
Source name Fetal lung, 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 lung 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 7.779829
1415671_at 8.66329
1415672_at 9.02554
1415673_at 5.553616
1415674_a_at 7.819682
1415675_at 6.805981
1415676_a_at 8.917385
1415677_at 7.410565
1415678_at 8.198826
1415679_at 9.648922
1415680_at 7.702736
1415681_at 7.890757
1415682_at 5.838944
1415683_at 8.623108
1415684_at 5.783547
1415685_at 6.490113
1415686_at 8.570702
1415687_a_at 9.491339
1415688_at 8.701554
1415689_s_at 6.487759

Total number of rows: 45037

Table truncated, full table size 893 Kbytes.




Supplementary file Size Download File type/resource
GSM326986.CEL.gz 3.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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