|
| Status |
Public on Aug 19, 2009 |
| Title |
Rat2_Control_0 |
| Sample type |
RNA |
| |
|
| Source name |
Rat Pool 2, vehicle control
|
| Organism |
Rattus norvegicus |
| Characteristics |
Organism: Sprague Dawley Rats
Strain: Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA
Tissue: Liver
Gender: Female
Chemical: Vehicle Control (0.5% DMSO)
Dose: NA
|
| 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 2, vehicle control
|
| 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.
|
| |
|
| Submission date |
Jan 23, 2009 |
| Last update date |
Aug 19, 2009 |
| Contact name |
Erik A Carlson |
| E-mail(s) |
carlson@ge.com
|
| Organization name |
General Electric
|
| Street address |
1 Research Circle
|
| City |
Niskayuna |
| State/province |
NY |
| ZIP/Postal code |
12309 |
| Country |
USA |
| |
|
| Platform ID |
GPL85 |
| Series (2) |
| GSE14554 |
Toxicogenomic Comparison of TCDD and PCB 126 Responsiveness in Primary Rat Hepatocytes |
| GSE14555 |
Divergent Transcriptomic Responses to Aryl Hydrocarbon Receptor Agonists Between Rat and Human Primary Hepatocytes |
|
