|
| Status |
Public on Sep 18, 2009 |
| Title |
Wildtype-mouse-liver-TCDD-rep6 |
| Sample type |
RNA |
| |
|
| Source name |
Wildtype mouse liver, TCDD treated, 19 hours
|
| Organism |
Mus musculus |
| Characteristics |
background: C57BL/6J
gender: male
ahr: wildtype
age: 15 weeks
treatment: TCDD
tissue: liver
|
| Treatment protocol |
Mice were given a single dose of 1000 µg/kg TCDD or corn oil vehicle by gavage. TCDD initially was dissolved in ether and added to corn oil; the ether subsequently was evaporated off. TCDD was purchased from the UFA-Oil Institute (Ufa, Russia) and was >99% pure as determined by gas chromatography-mass spectrometry.
|
| Growth protocol |
Male Ahr–/– mice (15 weeks old) in a C57BL/6J background were obtained from The Jackson Laboratory (Bar Harbor, ME). Wild-type (Ahr+/+) male C57BL/6J mice (15 weeks old) were bred at the National Public Health Institute (Kuopio, Finland) from stock originally obtained from The Jackson Laboratory.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Liver was harvested 19 h after treatment, sliced, snap-frozen, and stored in liquid nitrogen until homogenization. Total RNA was extracted using RNeasy kits (QIAGEN, Valencia, CA) according to the manufacturer's instructions. DNase (QIAGEN) was added to the RNeasy elution column as recommended by the manufacturer. RNA yield was quantified by UV spectrophotometry, and RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
|
| Label |
biotin
|
| Label protocol |
Manufacturer's protocol.
|
| |
|
| Hybridization protocol |
Manufacturer's protocol.
|
| Scan protocol |
Manufacturer's protocol.
|
| Description |
AHRWT4T
|
| Data processing |
Array data were loaded into the R statistical environment (v2.8.1) using the affy package (v1.20.2) of the BioConductor open-source library. Array data was investigated for spatial and distributional homogeneity; all arrays were included in subsequent analyses. Liver and kidney data were separately pre-processed using the GCRMA algorithm (Irizarry et al. Nucleic Acids Research 2003 and Wu et al. Jeans Hopkins University Department of Biostatistics Working Papers 2004) as implemented in the gcrma package (v2.14.1) of BioConductor. Array data were associated with updated sequence-annotation using the mouse4302mmentrezg package (v11.0.1), which remaps each probe to a unique Entrez Gene ID (Dai et al. Nucleic Acids Research 2005).
|
| |
|
| Submission date |
Apr 27, 2009 |
| Last update date |
Apr 01, 2011 |
| Contact name |
Paul C Boutros |
| E-mail(s) |
Paul.Boutros@utoronto.ca
|
| Organization name |
Ontario Institute for Cancer Research
|
| Street address |
101 College Street, Suite 800
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 0A3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL8492 |
| Series (2) |
| GSE15858 |
The Aryl Hydrocarbon Receptor Regulates Tissue-Specific Dioxin-Dependent and Dioxin-Independent Gene Batteries: Liver |
| GSE15859 |
The Aryl Hydrocarbon Receptor Regulates Tissue-Specific Dioxin-Dependent and Dioxin-Independent Gene Batteries |
|
| Relations |
| Reanalyzed by |
GSE26498 |
