Organism: Sprague Dawley Rats Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA Tissue: Liver Gender: Female Chemical: TCDD Dose: -8logM
Treatment protocol
See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
Growth protocol
See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
Extracted molecule
total RNA
Extraction protocol
See Silkworth et al. (2005). Toxicol. Sci. 87(2), 508-519
Label
biotin
Label protocol
Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
Hybridization protocol
GeneChips were hybridized according to the standard Affymetrix protocol
Scan protocol
GeneChips were scanned according to the standard Affymetrix protocol
Description
Rat Pool 1, -8logM TCDD
Data processing
All .CEL files (within each species) were pre-processed using the default settings of the justGCRMA function of gcrma package version 2.8.0 (Wu et al., 2004) as implemented in R. This function background corrects perfect-match probe intensities using probe sequence information, log2-transforms the data, quantile normalizes across the arrays, and summarizes probe intensities via the robust multiarray average (RMA) method (Irizarry et al., 2003) to give an intensity value (log2 scale) for each probe set.
