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Sample GSM398215 Query DataSets for GSM398215
Status Public on Sep 18, 2009
Title Wildtype-mouse-kidney-CornOil-rep2
Sample type RNA
 
Source name Wildtype mouse kidney, corn oil treated, 19 hours
Organism Mus musculus
Characteristics background: C57BL/6J
gender: male
ahr: wildtype
age: 15 weeks
treatment: Corn oil
tissue: kidney
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 Kidney 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 C5705
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)
GSE15857 The Aryl Hydrocarbon Receptor Regulates Tissue-Specific Dioxin-Dependent and Dioxin-Independent Gene Batteries: Kidney
GSE15859 The Aryl Hydrocarbon Receptor Regulates Tissue-Specific Dioxin-Dependent and Dioxin-Independent Gene Batteries
Relations
Reanalyzed by GSE26498

Data table header descriptions
ID_REF
VALUE GCRMA-normalized signal intensity

Data table
ID_REF VALUE
100009600_at 2.148423809
100012_at 2.148423809
100017_at 5.700059642
100019_at 5.014979251
100034251_at 2.528659569
100036521_at 9.218080445
100037258_at 9.937584431
100037278_at 2.148620015
100038570_at 2.463533213
100038635_at 2.148423809
100038887_at 12.34662831
100038959_at 2.148423809
100039027_at 2.148423809
100039094_at 2.148423809
100039235_at 2.148423809
100039282_at 2.148423809
100039284_at 3.2198675
100039307_at 2.148423809
100039332_at 2.148423809
100039359_at 2.162799769

Total number of rows: 16395

Table truncated, full table size 340 Kbytes.




Supplementary file Size Download File type/resource
GSM398215.CEL.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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