Investigation Title	Transcription profiling of human transplanted intestine before signs of rejects and when there was signs of actue cellular rejection	
Comment[AdditionalFile:XLS]	E-GEOD-5838.hybs.xls
Comment[Submitted Name]	Expression data from transplanted intestine bifor signs of rejection, and when their was signs of rejection	
Experimental Design	unknown_experiment_design_type	transcription profiling by array	
Experimental Design Term Source REF		EFO	
Comment[AEMIAMESCORE]	3	
Comment[ArrayExpressReleaseDate]	2008-04-03	
Comment[SecondaryAccession]	GSE5838	
Comment[ArrayExpressAccession]	E-GEOD-5838	
Comment[MAGETAB TimeStamp_Version]	2010-08-06 17:49:24 Last Changed Rev: 13058	
Experimental Factor Name	
Experimental Factor Type	
Experimental Factor Term Source REF	
Person Last Name	Elias	
Person First Name	Georg	
Person Mid Initials	
Person Email	georg.elias@umassmed.edu	
Person Phone	
Person Fax	
Person Address	Cell Transplant/ Cicalese, Surgery/ Transplant, UMASSMED, 377 plantation St/ Biotech 4, worcester, 01605, USA	
Person Affiliation	UMASSMED	
Person Roles	submitter	
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Date of Experiment	
Public Release Date	2008-04-03	
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Experiment Description	Acute cellular rejection (ACR) is the major cause of intestinal graft loss. Little is known about the genetic response occurring in small bowel transplantation (SBTx) during ACR. We report the case of a 44 year-old female with short gut syndrome following multiple surgeries for familial adenomatous polyposis that underwent living-related SBTx. We obtained for the first time a gene expression profile of the intestinal graft during ACR. Microarray analysis revealed increased transcript levels for genes that match identically to an IFN? signature reported for activated plasmacytoid dendritic cells and T-cell chemotaxis and cytolysis correlating with the diagnosis of ACR. Experiment Overall Design: sam1, sam2, sam3 (without signs of rejection) Experiment Overall Design: sam4, sam5, sam6 (with signs and symptoms of rejection , histology showed increasing lymphocyte infiltration in the lamina propria and epithelium)	
Protocol Name	P-5838-4	P-5838-2	P-5838-1	P-5838-3	
Protocol Type	nucleic_acid_extraction	labeling	hybridization	feature_extraction	
Protocol Description	RNeasy micro kit Qiagen, Valencia, CA, USA  Cat No 75142 according to the manufacturer's instructions.	Biotinylated cRNA were prepared according to the standard  BioArray RNA IVT labeling kit Enzo Life Science, Farmingdale, NY, USA	Following fragmentation, 10 microg of cRNA were hybridized on 45 C on Affymetrix HG-U133_Plus_2 human GeneChip, GeneChips were washed and stained in the Affymetrix Fluidics according to their protocol, EukGE-WS2v4_450	GeneChips were scanned using Pixel Size 1.56,  Filter 570, Scanner ID    50208790,   Scanner Type   M10	
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Protocol Term Source REF				The MGED Ontology	
SDRF File	E-GEOD-5838.sdrf.txt	
Term Source Name	mo	The MGED Ontology	ArrayExpress	EFO	The MGED Ontology	
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	http://www.ebi.ac.uk/efo/	http://mged.sourceforge.net/ontologies/MGEDontology.php	
Term Source Version