|
| Status |
Public on Sep 06, 2012 |
| Title |
B6_12_1 |
| Sample type |
RNA |
| |
|
| Source name |
WT mouse at week 12
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: B6
genotype: wild-type
gender: male
tissue: preputial gland duct
treatment: oral benzo[a]pyrene (BaP)
treatment duration: 12 weeks
|
| Treatment protocol |
Male mice of the three genotypes (75 mice total per genotype) were begun on the benzo[a]pyrene (BaP) diet at 6 weeks of age. BaP was added with the corn oil-soaked food such that the mice ingested approximately 12.5 mg/kg/day. Groups of N=15 for each genotype were killed at zero, 4, 8, 12 and 16 weeks, and preputial glands were dissected free of surrounding tissue.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Snap-frozen preputial glands (N=2 mice per group) from WT, Cyp1a1KO and Cyp1a1/1b1 DKO males treated with BaP at 0, 4, 8, 12, and 16 weeks were allowed to thaw overnight at -20oC with RNAlater®-ICE reagent prior to homogenization using Tri-Reagent. RNA isolation was performed using Qiagen RNeasy mini-kits.
|
| Label |
biotin
|
| Label protocol |
Ovation Pico WTA System (NuGEN, San Carlos, CA) following the manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Used the Affymetrix GeneChip hybridization and stain kit following the manufacturer's instructions.
|
| Scan protocol |
The GeneChips are scanned with Affymetrix GeneChip Scanner 3000 7G Plus using Affymetrix GeneChip Command Console 3.2.3.1515 software and Affymetrix preset settings.
|
| Description |
N7
Gene expression from WT at 12 weeks.
|
| Data processing |
Microarray data was preprocessed using RMA implemented in R with a BrainArray custom CDF (Entrez Gene, version 13).
|
| |
|
| Submission date |
Sep 05, 2012 |
| Last update date |
Sep 06, 2012 |
| Contact name |
Mario Medvedovic |
| Organization name |
University of Cincinnati
|
| Department |
Department of Environmental Health
|
| Lab |
Laboratory for Statistical Genomics and Systems Biology
|
| Street address |
3223 Eden Av. ML 56
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45267-0056 |
| Country |
USA |
| |
|
| Platform ID |
GPL11078 |
| Series (1) |
| GSE40633 |
Oral Benzo[a]pyrene in Cyp1a1/1b1(-/-) Double-Knockout Mice: Microarray Analysis During Squamous Cell Carcinoma Formation in Preputial Gland Duct |
|
