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Sample GSM306952 Query DataSets for GSM306952
Status Public on Mar 13, 2009
Title Liver_3mgRDX_0hr_rep1
Sample type RNA
 
Source name liver, 3 mg RDX, 0 hr
Organism Rattus norvegicus
Characteristics Sprague Dawley rats, male, 300-400 g
Treatment protocol Dosing capsules were filled by weighing pure RDX into size 9 gel capsules (Torpac, Fairfield, NJ). Capsules were then individually stored in dark glass sample bottles for up to two days in a refrigerator until required for dosing. At the time of dosing animals weighing 300-400 g were administered a one time dose of pure RDX in a gel capsule according to the manufacturer's instructions. Doses were calculated, based on previous work, so as not to induce seizure, and animals were observed over the first hour to confirm lack of seizure.
Extracted molecule total RNA
Extraction protocol Frozen tissue was homogenized in Tri Reagent (Sigma Chemical Company, St. Louis, MO) and the RNA extracted according to the manufacturer's protocol. RNA was further purified using RNeasy columns (Qiagen, Valencia, CA). The quality and amount of RNA was monitored throughout processing with an Agilent Bioanalyzer (Agilent, Palo Alto, CA) and a NanoDrop® ND-1000 UV-Vis Spectrophotometer (Nanodrop Technologies, Rockland, DE).
Label biotin
Label protocol 10 µg of mRNA was used to generate first-strand cDNA using a T7-linked oligo(dT) primer. After second-strand synthesis, in vitro transcription was performed with biotinylated UTP and CTP (Enzo Kits from Affymetrix).
 
Hybridization protocol Spike controls were added to 15 µg fragmented cRNA before overnight (16hr) hybridization using 10 µg of cRNA. Arrays were washed and stained with streptavidin-phycoerythrin before being scanned on an Affymetrix GeneChip Scanner.
Scan protocol After scanning, array images were assessed by eye to confirm scanner alignment and the absence of significant bubbles or scratches on the chip surface. The 3'/5' ratios for GAPDH and B-actin were checked for quality. BioB, BioC, BioD and CreX spike controls were also examined to determine sample quality. All arrays were scaled to a target intensity of 150 using Affymetrix GeneChip Operating System (GCOS) software.
Description pair-housed; one week acclimatization period; 12/12 light/dark cycle; food and water provided ad libitum.
Data processing Data was imported into Gensifter (VizX Laboratories, Seattle, WA) (www.gensifter.net) and normalized using Robust Multiarray Averaging (RMA). Data was also imported into Partek Genomics Solutions (Partet, St. Louis, MO), normalized using RMA, and visualized using principal component analysis (PCA).
 
Submission date Jul 22, 2008
Last update date Mar 13, 2009
Contact name James F Dillman
E-mail(s) james.f.dillman2.civ@mail.mil
Phone 4104361723
Organization name U.S. Army Medical Research Institute of Chemical Defense
Department Cell and Molecular Biology Branch
Lab Molecular Toxicology Team
Street address 3100 Ricketts Point Rd
City Aberdeen Proving Ground
State/province MD
ZIP/Postal code 21010-5400
Country USA
 
Platform ID GPL1355
Series (1)
GSE12196 Rat exposure to RDX (3mg/kg or 18mg/kg; 0, 4, 24, 48 hr)

Data table header descriptions
ID_REF
VALUE RMA normalized signal intensities

Data table
ID_REF VALUE
1367452_at 10.2174
1367453_at 10.3426
1367454_at 10.0761
1367455_at 10.4879
1367456_at 9.79637
1367457_at 9.99504
1367458_at 8.98714
1367459_at 11.8684
1367460_at 12.0637
1367461_at 8.98571
1367462_at 9.26337
1367463_at 11.7187
1367464_at 9.05469
1367465_at 10.3555
1367466_at 9.89404
1367467_at 12.0513
1367468_at 9.57831
1367469_at 11.985
1367470_at 11.5689
1367471_at 9.81454

Total number of rows: 31099

Table truncated, full table size 577 Kbytes.




Supplementary file Size Download File type/resource
GSM306952.CEL.gz 2.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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