Comment[ArrayExpressAccession]	E-GEOD-41524
MAGE-TAB Version	1.1						
Public Release Date	2013-10-01
Investigation Title	Gene expression in Dupuytren's disease						
Comment[Submitted Name]	Gene expression in Dupuytren's disease
Experiment Description	Dupuytren's disease (DD) is a classic example of pathological fibrosis which results in a debilitating disorder affecting a large sector of the human population. It is characterized by excessive local proliferation of fibroblasts and over-production of collagen and other components of the extracellular matrix (ECM) in the palmar fascia. The fibrosis progressively results in contracture of elements between the palmar fascia and skin causing flexion deformity or clawing of the fingers and a severe reduction in hand function. While much is known about the pathogenesis and surgical treatment of DD, little is known about the factors that cause its onset and progression, despite many years of research. Gene expression patterns in DD patients now offers the potential to identify genes that direct the pathogenesis of DD.  In this study, we used primary cultures of fibroblasts derived from excisional biopsies of fibrotic tissue from DD patients to compare the gene expression profiles on a genome-wide basis with normal control fibroblasts. Our investigations have identified genes that may be involved with DD pathogenesis including some which are directly relevant to fibrosis. In particular, these include significantly reduced expression levels of three matrix metallopeptidases (MMP1, MMP3, MMP16), follistatin, and STAT1, and significantly increased expression levels of fibroblast growth factors (FGF9, FGF11), a number of collagen genes and other ECM genes in DD patient samples. Many of these gene products are known to be involved in fibrosis, tumour formation and in the normal processes of tissue remodelling. In addition, alternative splicing was identified in some DD-associated genes. These highly sensitive genomic investigations provide new insight into the molecular mechanisms that may underpin the development and progression of DD. Four exon arrays of DD primary fibroblasts derived from fibrotic tissue were compared to fibroblasts derived from skin punch biopsies from individuals who did not show DD symptoms.						
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	Sprung	Sprung	Forrester	Temple-Smith			
Person First Name	Carl	Carl	Helen	Peter			
Person Mid Initials		N	B				
Person Email	carl.sprung@monash.edu						
Person Affiliation	Monash University						
Person Address	MIMR, Monash University, 27-31 Wright St, Clayton, Australia						
Person Roles	submitter						
Protocol Name	P-GSE41524-1	P-GSE41524-5	P-GSE41524-6	P-GSE41524-2	P-GSE41524-3	P-GSE41524-4	P-GSE41524-7
Protocol Description	Data were processed using aroma.affymetrix (R package). RMA background correction was applied to probe intensities, and gene-level expression were quantile normalized. Only the Core probesets have been used for analysis. Transcript assignments are based on genome build hg19. HuEx-1_0-st-v2.na32.hg19.probeset.csv Probe group file: HuEx-1_0-st-v2.r2.pgf Meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps ID_REF =  VALUE = RMA expression value	GeneChip Human Exon 1.0 ST Array analysis was performed on samples from 4 DD patients and 6 control patients (10 arrays total) as per the GeneChip Whole Transcript (WT) Sense Target labelling assay instructions (Affymetrix, Santa Clara, CA, USA). The rRNA from 1 microgram of total RNA was reduced using a RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen, Carlsbad, CA, USA).	The exact prodedure of the 'GeneChip Whole Transcript (WT) Sense Target labelling assay Manual' (Affymetrix) was followed.	No treatments were given.	Primary fibroblasts were maintained in DMEM plus serum at 37oC and 5% CO2.	Ten million fibroblasts from each DD and control cell line were pelleted, resuspended in 3 ml PBS with an equal volume of Trizol (Invitrogen, Carlsbad, CA, USA), mixed and incubated at room temperature for 15 minutes. Chloroform was then added and the mixture was centrifuged to separate the aqueous from the organic layers. The aqueous layer was mixed with an equal volume of 70 percent ethanol and layered on to an RNeasy column (Qiagen, Venlo, The Netherlands). The RNA extraction was continued by using the RNeasy method as per the manufacturer's recommendation except that the procedure was started at the step where Buffer RW1 is added. RNA concentration and integrity were determined using a Bioanalyzer (Agilent, Santa Clara, CA, USA). RNA was determined to be high enough quality for exon array analysis if a minimum RIN of 8.5 was obtained.	Chips were scanned with an Affymetrix GeneChip Scanner 3000 7G.
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	DISEASE STATE						
Experimental Factor Type	disease state						
Comment[SecondaryAccession]	GSE41524						
Comment[GEOReleaseDate]	2013-10-01						
Comment[ArrayExpressSubmissionDate]	2012-10-11						
Comment[GEOLastUpdateDate]	2013-10-02						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-41524.sdrf.txt