Comment[ArrayExpressAccession]	E-GEOD-46300				
MAGE-TAB Version	1.1				
Public Release Date	2015-11-01				
Investigation Title	Classifying distinct grades of human non-alcoholic fatty liver disease employing a systems biology approach				
Comment[Submitted Name]	Classifying distinct grades of human non-alcoholic fatty liver disease employing a systems biology approach				
Experiment Description	With an estimated prevalence of about 30% in western countries non-alcoholic fatty liver disease (NAFLD) is a major public health issue [PMID: 18956290]. NAFLD is associated with the metabolic syndrome of insulin resistance, obesity, glucose intolerance. Although many studies are pointing to an induction of insulin resistance by NAFLD causality between both phenotypes is not fully clarified. Furthermore, mechanisms leading to strongly differing progression of NAFLD have to be elucidated which range from mild steatosis up to severe steatohepatitis. Steatohepatitis might even result in liver cirrhosis and hepatocellular carcinoma. Additional complexity is introduced into the understanding of the disease by recent studies providing evidence for a direct development of carcinoma from steatosis without the formerly assumed intermediary phase of cirrhosis. Here, we investigate liver samples from patients with varying severities of steatosis in an integrative approach employing transcriptomics, serum biomarker profling, metabolomics data and systems biology models. Total RNA obtained from hepatocytes derived from nine obese patients with distinct grades of steatosis. This dataset is part of the TransQST collection.				
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	Wruck	Justyna			
Person First Name	Wasco	Jozefczuk			
Person Email	wasco.wruck@med.uni-duesseldorf.de				
Person Affiliation	Universitatklinikum Dusseldorf				
Person Address	Universitatklinikum Dusseldorf, Moorenstr. 5, Dusseldorf, Germany				
Person Roles	submitter				
Protocol Name	P-GSE46300-1	P-GSE46300-3	P-GSE46300-4	P-GSE46300-2	P-GSE46300-5
Protocol Description	The data were normalised using rank invariant normalisation with BeadStudio version 3 (Illumina) ID_REF =  VALUE = rank invariant normalized Detection Pval = 	Illumina Gene Expression protocols contain a first- and second-strand reverse transcription step, followed by a single in vitro transcription (IVT) amplification that incorporates biotin-labeled nucleotides. Subsequent steps include array hybridization, washing, blocking, and streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively detected for downstream analysis.	Standard Illumina hybridization protocol	The RNA was isolated using RNeasy Mini Kit (Quiagen), and DNase digestion (RNase-free DNase Set, Quiagen) has been applied on the columns during isolation.	Standard Illumina scanning protocol
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	disease staging				
Experimental Factor Type	disease staging				
Comment[SecondaryAccession]	GSE46300				
Comment[GEOReleaseDate]	2015-11-01				
Comment[ArrayExpressSubmissionDate]	2013-04-23				
Comment[GEOLastUpdateDate]	2015-11-01				
Comment[AEExperimentType]	transcription profiling by array				
Comment[AdditionalFile:Data1]	GSE46300_non_normalized.txt				
SDRF File	E-GEOD-46300.sdrf.txt				
					
Publication Title	Multi-omic profiles of human non-alcoholic fatty liver disease tissue highlight heterogenic phenotypes				
Publication Author List	Wasco Wruck,  Karl Kashofer, Samrina Rehman, Andriani Daskalaki, Daniela Berg, Ewa Gralka, Justyna Jozefczuk, Katharina Drews, Vikash Pandey, Christian Regenbrecht, Christoph Wierling, Paola Turano, Ulrike Korf, Kurt Zatloukal, Hans Lehrach, Hans V. Westerhoff and James Adjaye				
PubMed ID	26646939				
Publication DOI	10.1038/sdata.2015.68