Comment[ArrayExpressAccession]	E-GEOD-18257
Investigation Title	Transcriptional profiling of the rat hypothalamus response to TCDD
Comment[Submitted Name]	Transcriptional profiling of the rat hypothalamus response to TCDD
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Experimental Design	transcription profiling by array
Experimental Design Term Source REF	EFO
Public Release Date	2009-11-23
Experiment Description	Rodents exposed to the environmental contaminant, TCDD, suffer from a number of acute and chronic toxicities, including lethality and a wasting syndrome. Hypothesizing that the wasting syndrome may be caused by changes in neural control of energy flux and metabolism, we profiled the transcriptional response of rat hypothalamus to TCDD. We employed two separate rat strains: the Long-Evans strain is sensitive to TCDD toxicities while the Han/Wistar strain is over four orders of magnitude more resistant. Surprisingly, few transcriptional changes were induced by TCDD in either strain. Only four genes were altered in Long-Evans rats, including three classic TCDD-responsive genes: Cyp1a1, Cyp1b1, and Nqo1. These three genes were also altered in Han/Wistar rats, along with 133 additional genes. However, the magnitudes of alteration of these additional genes was very modest, with most changes well below two-fold in magnitude. We therefore concluded that rat hypothalamus is mostly refractory to TCDD exposure, at least at the doses and time-points surveyed here. Two strains, each with drug-treated vs. vehicle-control							
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Term Source Name	EFO
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Person Last Name	Boutros	Boutros	Okey	Pohjanvirta				
Person First Name	Paul	Paul	Allan	Raimo				
Person Mid Initials	C	C	B					
Person Email	Paul.Boutros@utoronto.ca							
Person Affiliation	Ontario Institute for Cancer Research							
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Person Address	Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario, Canada							
Person Roles	submitter							
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Protocol Name	P-GSE18257-1	P-GSE18257-6	P-GSE18257-3	P-GSE18257-8	P-GSE18257-7	P-GSE18257-2	P-GSE18257-4	P-GSE18257-5
Protocol Description	ID_REF = <br>VALUE = RMA-normalized signal intensities	Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada	Animals were grown in a 12h/12h light/dark cycle housed in groups of 4 rats in suspended stainless-steel wire-mesh cages with pelleted R36 feed and tap water. The temperature was 21 +/- 1 degree Celcius and the relative humidity 50% +/- 10%.	Quantitated array data (CEL files) were loaded into the R statistical environment (v2.9.1) using the Affy package (v1.22.1) of the BioConductor library. Data was investigated for spatial and distributional homogeneity, then pre-processed with the RMA algorithm (Irizarry et al. NAR). We employed an updated and remapped mapping of Probes to Entrez Gene IDs as implemented in the R package rat2302rnentrezgcdf (v12.0.0).	Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada	TCDD treated animals were treated with 100 ug/kg TCDD by oral gavage.	Total RNA was extracted using Qiagen RNeasy kits according to the manufacturer’s instructions (Qiagen, Mississauga, Canada). Total RNA yield was quantified by UV spectrophotometry and RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).	Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada
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Protocol Type	bioassay_data_transformation	hybridization	grow	feature_extraction	image_aquisition	specified_biomaterial_action	nucleic_acid_extraction	labeling
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Experimental Factor Name	STRAIN	TCDD DOSE	AGE					
Experimental Factor Type	strain	tcdd dose	age					
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Comment[SecondaryAccession]	GSE18257							
Comment[GEOLastUpdateDate]	2009-09-27
Comment[GEOReleaseDate]	2009-11-24
Comment[ArrayExpressSubmissionDate]	2009-09-23
SDRF File	E-GEOD-18257.sdrf.txt