Comment[ArrayExpressAccession]	E-GEOD-58979
MAGE-TAB Version	1.1						
Public Release Date	2015-08-04
Investigation Title	Gene expression in subcutaneous and visceral fat predicts liver histology in morbidly obese patients						
Comment[Submitted Name]	Gene expression in subcutaneous and visceral fat predicts liver histology in morbidly obese patients
Experiment Description	Nonalcoholic fatty liver disease (NAFLD) has become the most common cause of liver disease affecting 20-30% of the population in developed countries. NAFLD is strongly associated with abdominal obesity and is recognized as the hepatic manifestation of the metabolic syndrome. In a subgroup of patients with NAFLD inflammation and fibrosis develops, this so-called Non-Alcoholic Steatohepatitis (NASH) may progress to cirrhosis and hepatocellular carcinoma. A multi-hit hypothesis has been proposed in which during the first “hit” fat accumulation occurs in hepatocytes from excessive delivery of fatty acids from adipose tissue, in addition there is an imbalance in lipid synthesis and export. However, the reason why fat accumulation is subsequently followed by inflammation and fibrosis in some patients is poorly understood. We studied the role of inflammatory processes in visceral and subcutaneous fat at the transcriptional level using microarray in bariatric patients from whom the liver histology was available. Patients scheduled for bariatric surgery were recruited in two centers (Pretoria/South-Africa and Antwerpen/Belgium). At the time of the procedure, tissue samples of the visceral and subcutaneous fat were taken for molecular analysis as well as liver tissue for histology, also full biochemical data was collected. Patients were grouped according histology: group I (<5% steatosis), group II (NAFLD, 30-50% steatosis), group III (NASH) and group IV (NASH + fibrosis F2-F3). The following samples were used for microarray (number of 'patients' respectively for stages I-II-III-IV): visceral fat (9-7-7-5), subcutaneous fat (6-6-6-5). Microarrays were run in two batches (15xxx versus 17xxx CEL file samples; indicated in the description field). Samples from two patients (FN61; FN76) were put twice on array (15078+17881; 15064+17877) to verify and exclude batch effects.  Please note that, due to technical repeats with two patient samples, the number of 'visceral fat samples' for stages I-II-III-IV is 10-7-8-5.						
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	Van Delm	Du Plessis	van Pelt	van der Merwe			
Person First Name	Wouter	Johannie	Jos	Schalk			
Person Email	Nucleomics.Bioinformatics@vib.be						
Person Affiliation	Flanders Institute for Biotechnology (VIB)						
Person Phone	+32(0)16 37 31 26						
Person Address	Nucleomics Core, Flanders Institute for Biotechnology (VIB), Herestraat 49 Box 816, Leuven, Belgium						
Person Roles	submitter						
Protocol Name	P-GSE58979-1	P-GSE58979-5	P-GSE58979-6	P-GSE58979-2	P-GSE58979-3	P-GSE58979-4	P-GSE58979-7
Protocol Description	Data were normalized using RMA as implemented in the Affy package (version 1.40.0) of Bioconductor. Expression values are represented on a log2-scale. ID_REF =  VALUE = log2 RMA	RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).	A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix' PrimeView Human Gene Expression arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.	Samples collected during bariatric surgery	Clinical sample prior bariatric surgery	Rneasy kit (Qiagen)	To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
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	bmi	patientid	organism part	sex	age		
Experimental Factor Type	bmi	patientid	organism part	sex	age		
Publication Title	Association of Adipose Tissue Inflammation With Histologic Severity of Nonalcoholic Fatty Liver Disease.						
Publication Author List	du Plessis J, van Pelt J, Korf H, Mathieu C, van der Schueren B, Lannoo M, Oyen T, Topal B, Fetter G, Nayler S, van der Merwe T, Windmolders P, Gaal LV, Verrijken A, Hubens G, Gericke M, Cassiman D, Francque S, Nevens F, van der Merwe S						
PubMed ID	26028579						
Publication DOI	10.1053/j.gastro.2015.05.044						
Comment[SecondaryAccession]	GSE58979						
Comment[GEOReleaseDate]	2015-08-04						
Comment[ArrayExpressSubmissionDate]	2014-07-01						
Comment[GEOLastUpdateDate]	2015-08-04						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-58979.sdrf.txt