Comment[ArrayExpressAccession]	E-GEOD-54005
MAGE-TAB Version	1.1						
Public Release Date	2014-01-14
Investigation Title	Dextran sodium sulfate treatment of wild type and Pirc rats alters colonic normal tissue gene expression						
Comment[Submitted Name]	Dextran sodium sulfate treatment of wild type and Pirc rats alters colonic normal tissue gene expression
Experiment Description	Dextran sodium sulfate (DSS) causes inflammation in the gut similar to ulcerative colitis in humans.  Patients with ulcerative colitis have increased risk of developing colon cancer.  We sought to determine which genes are altered in the normal colonic epithelium, and which changes depend on the Pirc mutation. 97 day old (ACIxF344)F1 wild type and Pirc male rats either untreated or given 4% DSS in the drinking water from 40-47 and 54-61 days of age, housed in 12 hour light:12 dark, ad lib feeding.  Normal colonic tissue was collected from the distal colon at 97 days of age.						
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	Irving	Irving	Dove				
Person First Name	Amy	Amy	William				
Person Mid Initials		A	F				
Person Email	geo@ncbi.nlm.nih.gov						
Person Affiliation	University of Wisconsin-Madison						
Person Address	McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, 1400 University Avenue, Madison, WI, USA						
Person Roles	submitter						
Protocol Name	P-GSE54005-1	P-GSE54005-5	P-GSE54005-6	P-GSE54005-2	P-GSE54005-3	P-GSE54005-4	P-GSE54005-7
Protocol Description	Agilent Feature extraction versions 9.1 and 9.5 for background subtraction - localbackground and normalization Linear LOWESS.  No quantile normalization was deemed necessary by Partek software. ID_REF =  VALUE = background subtraction - localbackground and normalization Linear  LOWESS	Total RNA was amplified and labeled according to manufacturer instructions. Agilent One-Color Microarray-Based Gene Expression Analysis Agilent low RNA input linear amplification kit, PLUS	Agilent One-Color Microarray-Based Gene Expression Analysis 17hrs 65 deg celcius Surehyb chamber	Indicated animals given 4% DSS (500,000 MW) in drinking water from 40-47 and 54-61 days of age. Sacrificed and dissected at 97 days, samples homogenized in RLTplus and stored at -80C	Ad lib feeding and drinking. 12hours light:12hours dark.	Qiagen Qiashredder columns followed by Qiagen Allprep DNA/RNA Extraction Kit with optional on-the-column Dnase treatment	Agilent Technologies Scanner G2505B US22502567 5um 16bit
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	TREATMENT	GENOTYPE					
Experimental Factor Type	treatment	genotype					
Comment[SecondaryAccession]	GSE54005						
Comment[GEOReleaseDate]	2014-01-14						
Comment[ArrayExpressSubmissionDate]	2014-01-12						
Comment[GEOLastUpdateDate]	2014-01-16						
Comment[AEExperimentType]	transcription profiling by array						
Comment[AdditionalFile:Data1]	GSE54005_WT_Pirc_Fold_Changes.xls						
SDRF File	E-GEOD-54005.sdrf.txt