Comment[ArrayExpressAccession]	E-GEOD-41919
MAGE-TAB Version	1.1				
Public Release Date	2013-05-01
Investigation Title	Gene expression profiling in the cerebral cortex of patients with cirrhosis with and without hepatic encephalopathy				
Comment[Submitted Name]	Gene expression profiling in the cerebral cortex of patients with cirrhosis with and without hepatic encephalopathy
Experiment Description	Hepatic encephalopathy (HE) is a frequent complication of liver cirrhosis and is seen as the clinical manifestation of a low grade cerebral edema associated with oxidative-nitrosative stress, however, comprehensive data on HE-associated molecular derangements in human brain are lacking. In the present study we used a whole human genome micro-array approach for gene expression profiling in post mortem brain samples from cirrhotic patients with or without HE and non-cirrhotic controls. Altered expression levels were found for a total of 1012 genes in liver cirrhotic patients without and with HE and HE-characteristic gene expression changes were identified. Genes with altered expression pattern in HE were related oxidative stress, microglia activation, inflammatory signalling pathways, cellular proliferation and apoptosis. Despite an up-regulation of genes associated with microglia activation, pro-inflammatory cytokine mRNA profiles remained unchanged in the brain of patients with liver cirrhosis and HE as compared to controls. Interestingly, many genes counteracting pro-inflammatory signalling and inflammatory cytokine expression were up-regulated in the cerebral cortex of patients with liver cirrhosis and HE. It is concluded that pathogenetic mechanisms of HE deduced from cell culture and animal experiments, such as oxidative stress, altered Zn2+-homeostasis and microglia activation also apply to human brain from cirrhotic patients with HE.  The study also revealed a not yet recognized increased expression of genes antagonizing pro-inflammatory signalling and inflammatory cytokine expression. The dataset comprises 19 samples divided into three sample groups each representing a certain liver disease condition of humans.				
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	Goerg	GM-CM-6rg	Bidmon	HM-CM-$ussinger	
Person First Name	Boris	Boris	Hans	Dieter	
Person Mid Initials			J		
Person Email	Boris.Goerg@uni-duesseldorf.de				
Person Affiliation	Heinrich-Heine UniversitM-CM-$t DM-CM-<sseldorf				
Person Address	Clinic for Gastroenterology, Hepatology and Infectiology, Heinrich-Heine UniversitM-CM-$t DM-CM-<sseldorf, Moorenstrasse 5, DM-CM-<sseldorf, Germany				
Person Roles	submitter				
Protocol Name	P-GSE41919-1	P-GSE41919-3	P-GSE41919-4	P-GSE41919-2	P-GSE41919-5
Protocol Description	The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files. FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware, Rosetta error model; Lee Weng et al 2006). ID_REF =  VALUE = Quantile normalized signal intensity data (w/o controls) log2 transformed.	100 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturerM-bM-^@M-^Ys protocol.	Cy3 labeled cRNAs were hybridized overnight (17 hours, 65M-0C) to Agilent Whole Human Genome Oligo Microarrays (8x60K) using AgilentM-bM-^@M-^Ys recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37M-0C and a final wash step with acetonitrile for 30 sec at RT	The RNA was isolated by using standard RNA extraction protocols (RNeasy Mini Kit, Qiagen, Hilden Germany) and the RNA quality checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies). Only RNAs with calculated RNA Integrity Numbers (RIN) higher than 6 were accepted.	Fluorescence signals of the hybridized Agilent Microarrays were detected using AgilentM-bM-^@M-^Ys Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	DISEASE STATE				
Experimental Factor Type	disease state				
Comment[SecondaryAccession]	GSE41919				
Comment[GEOReleaseDate]	2013-05-01				
Comment[ArrayExpressSubmissionDate]	2012-10-30				
Comment[GEOLastUpdateDate]	2013-05-02				
Comment[AEExperimentType]	transcription profiling by array				
SDRF File	E-GEOD-41919.sdrf.txt