Comment[ArrayExpressAccession]	E-GEOD-58819
MAGE-TAB Version	1.1					
Public Release Date	2014-11-14
Investigation Title	Trichloroethylene-induced mRNA expression changes in B6C3F1 mouse liver					
Comment[Submitted Name]	Trichloroethylene-induced mRNA expression changes in B6C3F1 mouse liver
Experiment Description	To examine changes, if any, in the expression of mRNAs in the liver tissue of mice, we have employed whole genome microarray expression profiling as a discovery platform to identify genes responsive to Trichloroethylene (TCE) treatment.  In our results, the expression levels of 431 mRNAs were changed after TCE exposure, of which 291 were up-regulated and 140 were down-regulated. Using qPCR, we validated six of the mRNA expression changed genes, viz., Jun, Cdkn1a, Rad51b, Uhrf1, Svil and Ihh. Six B6C3F1 male mice were oral administrated with either corn oil or TCE (dissolved in corn oil, 1000mg/kg b.w per day) for 5 days.  The expression changes of mRNAs in TCE exposured mouse liver were screened by whole genome microarray expression profiling and were validated by qPCR.					
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl				
Person Last Name	Chen	Chen				
Person First Name	Tao	Tao				
Person Email	tchen@suda.edu.cn					
Person Affiliation	Soochow University					
Person Phone	8651265882273					
Person Address	Soochow University, 199 Ren-Ai-rd, SuZhou, JiangSu, China					
Person Roles	submitter					
Protocol Name	P-GSE58819-1	P-GSE58819-4	P-GSE58819-5	P-GSE58819-2	P-GSE58819-3	P-GSE58819-6
Protocol Description	Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze microarray images to obtain the raw data and basic analysis was completed using Genesrping. Differentially expressed genes were then identified through fold change as well as P value obtained from the t-test. The threshold set for up- and down-regulated genes was a fold change of >= 2.0 and a P value<= 0.05. ID_REF =  VALUE = processed Cy3 signal intensity (Agilent gProcessedSignal)	The Agilent Mouse Gene Expression kit (8x60K, Design ID：028005) was used which included 39430 mRNAs.	Total RNAs were transcribed to double strand cDNA and then, synthesized into cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray.	Adult B6C3F1 male mice were oral administrated with either corn oil or TCE for five days. Form each mouse, liver was excised rapidly, frozen in liquid nitrogen, and stored at -80oC.	Genomic DNA and RNA were purified using AllPrep DNA/RNA Mini Kit (Tiangen, Beijing, China). Turbo DNA-freeTM kit (Life Technologies, Shanghai, China) was used to remove genomic DNA contamination in purified RNA samples.	After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	treatment					
Experimental Factor Type	treatment					
Comment[SecondaryAccession]	GSE58819					
Comment[GEOReleaseDate]	2014-11-14					
Comment[ArrayExpressSubmissionDate]	2014-06-25					
Comment[GEOLastUpdateDate]	2014-11-16					
Comment[AEExperimentType]	transcription profiling by array					
Comment[AdditionalFile:Data1]	GSE58819_further-processed_data.txt					
SDRF File	E-GEOD-58819.sdrf.txt