|
| Status |
Public on Aug 15, 2007 |
| Title |
L-E rat liver: TCDD treated vs feed restricted |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Total RNA from L-E rat liver, TCDD treated for 96 h
|
| Organism |
Rattus norvegicus |
| Characteristics |
Strain: L-E
Sex: male
Treatment: 96hTCDD
Genotype: AhrWt/Wt
Age: 10-12 weeks
Tissue: liver
|
| Treatment protocol |
L-E rats were treated by gavage with a single dose of 100 µg/kg TCDD, corn oil vehicle, or their feed was restricted for 96 h.
|
| Growth protocol |
TCDD-sensitive L-E rats 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. Total RNA yield was quantified by UV spectrophotometry and RNA integrity was verified using an Agilent 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA).
|
| Label |
Hy3
|
| Label protocol |
Labeling of 2.5 µg of total RNA were performed using Exiqon’s MiRCury LNA array labeling kit (version 1.2) (Exiqon, Vedbaek, Denmark) according to the manufacturer's instructions.
|
| |
|
| Channel 2 |
| Source name |
Total RNA from L-E rat liver, feed restricted for 96 h
|
| Organism |
Rattus norvegicus |
| Characteristics |
Strain: L-E
Sex: male
Treatment: 96h feed restricted
Genotype: AhrWt/Wt
Age: 10-12 weeks
Tissue: liver
|
| Treatment protocol |
L-E rats were treated by gavage with a single dose of 100 µg/kg TCDD, corn oil vehicle, or their feed was restricted for 96 h.
|
| Growth protocol |
TCDD-sensitive L-E rats 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. Total RNA yield was quantified by UV spectrophotometry and RNA integrity was verified using an Agilent 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA).
|
| Label |
Hy5
|
| Label protocol |
Labeling of 2.5 µg of total RNA were performed using Exiqon’s MiRCury LNA array labeling kit (version 1.2) (Exiqon, Vedbaek, Denmark) according to the manufacturer's instructions.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed using Exiqon’s MiRCury LNA array hybridization kit (version 1.2) (Exiqon, Vedbaek, Denmark) according to the manufacturer's instructions. Slides were hybridized at 60ºC for 17 h.
|
| Scan protocol |
Arrays were scanned at 10-micron resolution on a GenePix 4000B Array Scanner (Axon instruments, Inc., Union City, CA) using auto-PMT calculation settings. Each element was located and analyzed with the GenePix Pro 6.0.1.26 software package.
|
| Description |
Liver was harvested from rats treated by gavage with a single dose of 100 µg/kg TCDD or corn oil vehicle or whose feed was restricted for 96 h
|
| Data processing |
Using LimmaGUI (v1.8.1; limma, v2.9.1; (Wettenhall and Smyth, 2004)), the array data were loaded into R statistical package (v2.4.0), investigated for spatial and distributional homogeneity, background subtracted (minimum method), normalized within-arrays (robust spline) and normalized between arrays (scale).
|
| |
|
| 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 |
GPL5531 |
| Series (2) |
| GSE8469 |
Micro-RNAs in Adult Long-Evans (Turku/AB) Rat Liver are Refractory to 96 Hours Dioxin Treatment |
| GSE8474 |
MicroRNAs in adult rodent liver and response to dioxin |
|
