|
| Status |
Public on Aug 01, 2012 |
| Title |
DBC_1 |
| Sample type |
RNA |
| |
|
| Source name |
Mouse skin exposed to dibenzo[def,p]chrysene (DBC), biological rep1
|
| Organism |
Mus musculus |
| Characteristics |
treatment: dibenzo[def,p]chrysene (DBC) 4 nmol (1.2 ug)
tissue: skin
strain: FVB/N
|
| Treatment protocol |
At 7.5 weeks of age, mice were shaved on their dorsal surface and allowed to rest 48 h to confirm that animals were in the resting phase of the hair growth cycle. The following initiation treatments were applied to groups of mice (N=4 or 5 biological replicates) by slowly pipetting solutions on the shaved area; toluene vehicle control (200 μl), benzo[a]pyrene (BAP) 400 nmol (100 μg), dibenzo[def,p]chrysene (DBC) 4 nmol (1.2 μg), or 1 of 3 PAH mixtures: Mix 1 (1 mg diesel particulate extract), Mix 2 (1 mg diesel particulate extract + 1 mg coal tar extract), or Mix 3(1 mg diesel particulate extract + 1 mg coal tar extract + 2 mg cigarette smoke condensate).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
In order to eliminate RNase degradation, epidermis and dermis layers were kept intact, removed as one piece and snap frozen in liquid nitrogen. A 1-cm2 section of frozen skin was placed in a 15-ml sterile, disposable conical homogenizer, VWR Scientific Inc. (San Francisco, CA.) and homogenized in 2 ml Trizol® reagent. RNA was extracted according to the manufacturer’s instructions followed by a clean-up step using an RNeasy® mini kit, Qiagen Corp., Valencia, CA.
|
| Label |
Cy3
|
| Label protocol |
The RNA was labeled with Agilent’s 2 color Quickamp kit.
|
| |
|
| Hybridization protocol |
Samples were hybridized to the Agilent 8X60 K mouse array following manufacturer instructions.
|
| Scan protocol |
Agilent Technologies Scanner G2505C 3um 20bit
|
| Description |
Gene expression in mouse skin 12 hr post-initiation
|
| Data processing |
Raw Agilent intensity data were background subtracted and quantile-normalized by RMA summarization as described by (Bolstad et al., 2003). Statistical analysis was performed by one-way ANOVA for unequal variances (Welch’s ANOVA) with Tukey’s posthoc test and 5% FDR.
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| |
|
| Submission date |
Jul 18, 2012 |
| Last update date |
Aug 01, 2012 |
| Contact name |
Susan C. Tilton |
| E-mail(s) |
Susan.Tilton@oregonstate.edu
|
| Organization name |
Oregon State University
|
| Department |
AG Envr & Molec Toxicology
|
| Street address |
1007 ALS Bldg
|
| City |
Corvallis |
| State/province |
OR |
| ZIP/Postal code |
97331 |
| Country |
USA |
| |
|
| Platform ID |
GPL10787 |
| Series (1) |
| GSE39455 |
Polycyclic aromatic hydrocarbons as skin carcinogens: Comparison of benzo[a]pyrene, dibenzo[def,p]chrysene and three environmental mixtures in the FVB/N mouse |
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