|
| Status |
Public on Jan 19, 2011 |
| Title |
RatLiver_SeDef_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
liver, Se deficient
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: liver
treatment: Se deficient
|
| Treatment protocol |
Animals were anesthetized with ether and livers were perfused in situ with ice-cold 0.15 M potassium chloride. Liver and kidney were removed and snap-frozen in liquid nitrogen for later RNA analysis.
|
| Growth protocol |
Weanling mice or rats were housed in hanging wire cages and fed Se-deficient diets supplemented with up to 5 ug Se/g diet for 35 or 28 days, respectively
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed on frozen tissue according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared with ENZO IVT kits from 5 ug cDNA for mouse samples and with MessageAmp Biotin-Enhanced IVT kits from 3 ug total RNA for rat samples
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Rat Genome 230 2.0 or Mouse Genome 430 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 following the EukGE_WS2v5_450 fluidics protocol.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GC 3000 G7 Scanner and image data was extracted using the AFX Expression Console software.
|
| Description |
Gene expression from liver of a rat fed a Se-deficient diet for 28 days
|
| Data processing |
The data were analyzed in R/Bioconductor using the GCRMA algorithm.
|
| |
|
| Submission date |
Aug 31, 2010 |
| Last update date |
Jan 19, 2011 |
| Contact name |
Roger A Sunde |
| E-mail(s) |
sunde@nutrisci.wisc.edu
|
| Phone |
608-262-4044
|
| Organization name |
University of Wisconsin
|
| Department |
Nutritional Sciences
|
| Street address |
1415 Linden Dr
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706-1527 |
| Country |
USA |
| |
|
| Platform ID |
GPL1355 |
| Series (1) |
| GSE23895 |
Selenium toxicity but not deficient or super-nutritional selenium status vastly alters the transcriptome in rodents |
|
