Comment[ArrayExpressAccession]	E-GEOD-15090
Public Release Date	2009-03-04					
Investigation Title	Gene expression profiles in muscle tissue from FSHD patients					
Comment[Submitted Name]	Gene expression profiles in muscle tissue from FSHD patients
Experiment Description	Muscle biopsies from biceps and deltoid were taken from 5 patients with FSHD, 5 asymptomatic carriers and 5 normal controls. The genome-wide expression patterns were compared using Affymetrix U133 Plus 2.0 chips.  Keywords: Facioscapulohumeral, FSHD, muscular dystrophy Gene expression profiles were generated for 15 individuals (5 affected patients, 5 asymptomatic carriers and 5 healthy controls)					
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Term Source Name	EFO
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Term Source File	http://www.ebi.ac.uk/efo/efo.owl					
Person Last Name	Kho	Kho	Arashiro	Kunkel	Zatz	
Person First Name	Alvin	Alvin	Patricia	Louis	Mayana	
Person Mid Initials	T.	T				
Person Email	alvin_kho@hms.harvard.edu					
Person Affiliation	Children's Hospital Boston					
Person Phone	617-355-6393					
Person Fax	617-730-0921					
Person Address	Informatics Program, Children's Hospital Boston, 320 Longwood Avenue, Boston, MA, USA					
Person Roles	submitter					
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Protocol Name	P-GSE15090-1	P-GSE15090-5	P-GSE15090-4	P-GSE15090-2	P-GSE15090-3	P-GSE15090-6
Protocol Description	ID_REF = <br>VALUE = MAS 5 signal<br>ABS_CALL = <br>DETECTION_P-VALUE = 	The probe arrays were scanned using the Affymetrix GeneChip Scanner 7G.	15 micrograms of fragmented cRNA were hybridized to U133 Plus 2.0 chips for 16 hours at 45 M-0C, 60 rpm. The chips were washed and stained in the Affymetrix Fluidics Station 450, using instructions and reagents provided by Affymetrix.	Total RNA was isolated from muscle tissue using the TRIReagent method (Molecular Research Center, Inc.) following the manufacturerM-bM-^@M-^Ys protocol. Concentrations were determined using a NanoDrop 1000 spectrophotometer. Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual.	In vitro transcription (IVT) was performed using the GeneChip Expression Amplification Reagents kit following the standard Affymetrix protocols.	MAS5 algorithm
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Protocol Type	bioassay_data_transformation	image_aquisition	hybridization	nucleic_acid_extraction	labeling	feature_extraction
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Experimental Factor Name	ORGANISM PART	DISEASE STATUS	AGE	SEX	FAMILY	
Experimental Factor Type	organism part	disease status	age	sex	family	
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Publication Title	Transcriptional regulation differs in affected facioscapulohumeral muscular dystrophy patients compared to asymptomatic related carriers.					
Publication Author List	Arashiro P, Eisenberg I, Kho AT, Cerqueira AM, Canovas M, Silva HC, Pavanello RC, Verjovski-Almeida S, Kunkel LM, Zatz M					
PubMed ID	19339494					
Publication DOI	10.1073/pnas.0901573106					
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Comment[SecondaryAccession]	GSE15090					
Comment[GEOLastUpdateDate]	2012-04-11
Comment[AEExperimentType]	transcription profiling by array					
Comment[GEOReleaseDate]	2009-03-04
Comment[ArrayExpressSubmissionDate]	2009-03-03
SDRF File	E-GEOD-15090.sdrf.txt