|
| Status |
Public on Aug 15, 2007 |
| Title |
L-E_Liver_vehicle-control_19hr_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
L-E rat Liver vehicle-control 19hr
|
| Organism |
Rattus norvegicus |
| Characteristics |
Strain: L-E
Sex: male
Treatment: corn oil
Genotype: AhrWt/Wt
Age: 10-12 weeks
Tissue: liver
|
| Treatment protocol |
L-E and H/W rats were treated by gavage with a single dose of 100 µg/kg TCDD or corn oil vehicle for 19 hours
|
| Growth protocol |
TCDD-sensitive L-E rats (which express wildtype AHR) and TCDD-resistant H/W rats (with a deletion in the AHR transactivation domain, (Pohjanvirta et al., 1998)) were from breeding colonies of the National Public Health Institute, Division of Environmental Health, Kuopio, Finland.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from rat livers using the mirVana miRNA Isolation Kit (Ambion, Austin, TX) according to the manufacturer’s instructions except flashPAGE fractionation (Ambion) was not performed due to high technical variability. Small-population RNA (<200 nt) was enriched from mirVana-isolated total RNA according to manufacturer’s instructions. Total RNA yield was quantified by UV spectrophotometry and RNA integrity was verified using an Agilent 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy5
|
| Label protocol |
Two µg of purified small-population RNA from livers of L-E and H/W rats were labeled with a NHS-ester modified Cy5-fluorophore (GE Healthcare Bio-Sciences Corp., Piscataway, NJ) using the mirVana miRNA Labeling Kit (Ambion), according to the manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
Hybridization and washing were according to the manufacturer’s instructions (Ambion). A single labeled miRNA sample was hybridized on to each mirVana miRNA Bioarray. Slides were hybridized at 42ºC for 14 h.
|
| Scan protocol |
Arrays were scanned at 10-micron resolution on a PerkinElmer ScanArray microarray scanner (PerkinElmer Life and Analytical Sciences Inc., Waltham, MA) using a photomultiplier tube (PMT) setting of 60 and a laser power of 90. Each element was located and analyzed using the GenePix Pro 6.0.1.26 software package (Molecular Devices Corporation, Union City, CA).
|
| Description |
Liver was harvested from rats treated by gavage with a single dose of 100 µg/kg TCDD or corn oil vehicle for 19h
|
| Data processing |
Using LimmaGUI (version 1.8.1; limma, version 2.9.1; (Wettenhall and Smyth, 2004)), the array data were loaded into R statistical package (version 2.4.0), investigated for spatial and distributional homogeneity, background was subtracted, and pre-processed with the variance-stabilizing normalization algorithm (Huber et al., 2002).
|
| |
|
| Submission date |
Jul 13, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Ivy Moffat |
| E-mail(s) |
ivy.moffat@utoronto.ca
|
| Phone |
416-978-2207
|
| Fax |
416-978-6395
|
| Organization name |
University of Toronto
|
| Department |
Pharmacology
|
| Lab |
Dr. Allan B. Okey
|
| Street address |
1 King's College Circle, Medical Science Building Rm.4302
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5S 1A8 |
| Country |
Canada |
| |
|
| Platform ID |
GPL3444 |
| Series (2) |
| GSE8467 |
Micro-RNAs in Adult Rat Liver are Refractory to 19 Hours Dioxin Exposure |
| GSE8474 |
MicroRNAs in adult rodent liver and response to dioxin |
|
