|
| Status |
Public on Aug 10, 2007 |
| Title |
folatesufficientAs1ppm4 |
| Sample type |
RNA |
| |
|
| Source name |
ODC mouse skin samples from a mouse fed folatesufficientAs1ppm
|
| Organism |
Mus musculus |
| Characteristics |
samples were obtained from 6 treatment groups with 4 samples each ( 3 arsenic doses x 2 folate conditions)
|
| Treatment protocol |
Mice were fed either a folate deficient purified diet (AIN-76A) with vitamin free casein, corn oil and 1% succinyl sulfathiazole, or the same diet supplemented with 5 mg/kg folic acid (Dyets, Bethlehem, PA; product nos. 117757 and 117758).Mice on both diets were treated with 0, 1, or 10 ppm sodium arsenite in the drinking water for 30 days prior to euthanasia. Skin samples were harvested from the mid-back, flash frozen in liquid nitrogen, and stored at -80C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the TriReagent procedure (Molecular Research Center, Cincinnati, OH) and the Qiagen Rneasy mini RNA cleanup protocol (Qiagen, Valencia, CA)
|
| Label |
biotin-streptavidin-R-phycoerythrin
|
| Label protocol |
Samples were labeled according to the 2004 Affymetrix One-Cycle IVT Target Labeling protocol
|
| |
|
| Hybridization protocol |
Samples were hybridized according to the 2004 Affymetrix Standard Format Protocol
|
| Scan protocol |
Mouse 430 2.0 GeneChips were scanned according to 2004 Affymetrix protocol using a Affymetrix High Density GeneChip Scanner 3000
|
| Description |
gene expression data from ODC mouse skin samples
|
| Data processing |
Affymetrix GeneChip Operating System (GCOS) software was used for washing, staining, and scanning GeneChips. GCOS files were generated including quality control metric summaries. GCOS generated .cel files were used to calculate expression summaries in GeneSpring GX 7.3 using RMA normalization.
|
| |
|
| Submission date |
Aug 09, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Gail M Nelson |
| E-mail(s) |
nelson.gail@epa.gov
|
| Phone |
919-541-3095
|
| Organization name |
U.S. Environmental Protection Agency
|
| Street address |
109 TW Alexander Dr.
|
| City |
Research Triangle Park |
| State/province |
NC |
| ZIP/Postal code |
27711 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE8733 |
Folate deficiency enhances arsenic effects on ODC mouse skin gene expression |
|
| Relations |
| Reanalyzed by |
GSE119085 |
