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Sample GSM796809 Query DataSets for GSM796809
Status Public on Oct 05, 2011
Title Liver_rat_male_PBDE_rep4
Sample type RNA
 
Source name rat_male_50mg/kg DE71
Organism Rattus norvegicus
Characteristics strain background: Wistar/Han
age: rat (week 13)
gender: male
tissue: liver
pbde dose: high
Treatment protocol On PND 22, livers from five male and five female pups culled from the control and high dose groups were collected for toxicogenomic analysis (each pup came from a different dam). These animals were dosed through the day (PND 21) before liver tissue collection (PND 22). Liver samples were collected from 5 control female pups, 5 control male pups, 5 50 mg/kg female pups, and 5 50 mg/kg male pups. At week 13, 10 males from the 0 and 50 mg/kg groups were sacrificed and the liver tissue was collected for toxicogenomic analysis and histopathlogy (each animal came from a different dam in that dose group).
Growth protocol Time mated female Wistar/Han dams (CRL:WI (HAN)) were obtained from Charles River Laboratories (Raleigh, NC). Dams were dosed by gavage with 0 or 50 mg/kg DE71 in corn oil (dosing volume 5 ml/kg) from GD 6 through PND 21, 7 days per week. Direct dosing of pups began on and continued through PND 21 for 7 days per week until weaning. Weaning occurred on PND 21, which was designated as Day 1 of the 13-week portion of the study, and the day the pups were assigned to the 13-week portion of the study. On day one of the 13-week portion of the study dosing began on a 5 days/week schedule. Pups designated for toxicogenomic study were dosed through PND 21, the day prior to PND 22 liver sample collection. Tap water and NTP-2000 diet (Zeigler Brothers, Inc. Gardners, PA) was made available ad libitum (National Toxicology Program 2005a, b).
Extracted molecule total RNA
Extraction protocol A section of the liver was collected at necropsy, frozen and sent to the microarray processing unit where the liver was placed into RNAlater (Ambion, Inc., Austin, TX). RNA was extracted from liver using the QIAGEN Rneasy (QIAGEN, Valencia, CA). The RNA was analyzed for quantity and purity by UV analysis using the NanoDrop ND-1000 (NanoDropTechnologies, Wilmington, DE). Samples were concentrated using Microcon filters (Millipore, Billerica, MA). All samples were evaluated for RNA integrity by gel electrophoresis using the Flash Gel RNA cassette system (Lonza, Rockland, ME).
Label biotin
Label protocol Total RNA (50 ng) was used to synthesize double-stranded cDNA for each sample using Affymetrix GeneChipExpression 3'amplication two-cycle target labeling and control reagents (Affymetrix Inc. Santa Clara, CA). The cDNA served as a template to synthesize biotin-labeled antisense cRNA using an in vitro transcription (IVT) labeling kit. Labeled cRNA was fragmented and hybridized to the Affymetrix Rat Genome 230 2.0 Genechip Array.
 
Hybridization protocol Labeled cRNA was fragmented and hybridized to the Affymetrix Rat Genome 230 2.0 Genechip Array. Array hybridization, washing, and staining were performed according to the Affymetrix recommended protocol EuKGE_Ws2v5.
Scan protocol Affymetrix GeneChip Scanner 3000
Description liver from PBDE treated male rat
X100809.29_.Rat230_2..CEL
Data processing Data were processed using R/affy software. In brief, the RMA method adjusts the background of perfect match (PM) probes, applies a quantile normalization of the corrected PM values, and calculates final expression measures with the Tukey median polish algorithm.
 
Submission date Sep 15, 2011
Last update date Oct 05, 2011
Contact name Keith Shockley
Organization name NIEHS
Street address 111 TW Alexander Drive
City RTP
State/province NC
ZIP/Postal code 27709
Country USA
 
Platform ID GPL1355
Series (1)
GSE32156 Expression data from PBDE treated rats at PND22 and Week 13

Data table header descriptions
ID_REF
VALUE RMA normalized

Data table
ID_REF VALUE
1367452_at 10.15107093
1367453_at 10.33413916
1367454_at 10.79894056
1367455_at 12.08561015
1367456_at 12.32031475
1367457_at 9.512165724
1367458_at 8.70694031
1367459_at 12.40534236
1367460_at 12.11961297
1367461_at 10.6592372
1367462_at 10.53987422
1367463_at 11.13638223
1367464_at 9.980318822
1367465_at 10.39327808
1367466_at 10.17756341
1367467_at 11.77053869
1367468_at 9.534276356
1367469_at 12.42991922
1367470_at 10.99944786
1367471_at 9.096174174

Total number of rows: 31099

Table truncated, full table size 698 Kbytes.




Supplementary file Size Download File type/resource
GSM796809_100809-29_Rat230_2_.CEL.gz 2.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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