Comment[ArrayExpressAccession]	E-GEOD-7621		
Investigation Title	Transcription profiling of human substantia nigra from postmortem brain of Parkinsons disease patients (PD)		
Comment[Submitted Name]	Expression data of substantia nigra from postmortem human brain of Parkinson's disease patients (PD)		
Publication Title	A genomic pathway approach to a complex disease: axon guidance and Parkinson disease.		
Publication Author List	"Lesnick TG, Papapetropoulos S, Mash DC, Ffrench-Mullen J, Shehadeh L, de Andrade M, Henley JR, Rocca WA, Ahlskog JE, Maraganore DM"		
Publication DOI	10.1371/journal.pgen.0030098		
PubMed ID	17571925		
Publication Status	published		
Publication Status Term Source REF	EFO		
Publication Status Term Accession Number	EFO_0001796		
Experimental Design	disease_state_design	sex_design	co-expression_design
Experimental Design Term Source REF	The MGED Ontology	The MGED Ontology	The MGED Ontology
Experimental Factor Name	disease		
Experimental Factor Type	disease		
Person Last Name	ffrench-Mullen		
Person First Name	Jarlath		
Person Mid Initials	M.H.		
Person Email	jfmullen@genelogic.com		
Person Address	"CNS Program, GeneLogic, Inc., 610 Professional Drive, Gaithsburg, 20879, USA"		
Person Affiliation	"GeneLogic, Inc."		
Person Roles	submitter		
Public Release Date	2008-11-06		
Comment[AEExperimentDisplayName]	Transcription profiling by array of human substantia nigra from patients with Parkinson's disease		
Comment[AEExperimentType]	transcription profiling by array		
Comment[ArrayExpressSubmissionDate]	2007-04-25		
Comment[GEOReleaseDate]	2007-06-14		
Comment[SecondaryAccession]	GSE7621	GDS2821	
Experiment Description	We used microarrays to detail the global program of gene expression underlying Parkinson's disease Experiment Overall Design: Substantia nigra tissue from postmortem brain of normal and Parkinson disease patients were used for RNA extraction and hybridization on Affymetrix microarrays: 9 replicates for the controls and 16 replicates for the Parkinson's disease patients were used. Both cohorts included males and females.		
Protocol Name	P-G7621-2	P-G7621-1	P-G7621-3
Protocol Type	nucleic acid labeling protocol	growth protocol	nucleic acid extraction protocol
Protocol Description	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)."	"Brain tissue was removed with a Post-Mortem Interval (PMI) of 9.03±2.2 hr for Control samples and 7.05±1.25 hr for the PD samples, subsequently sectioned and frozen."	Trizol lysis extraction of total RNA was performed on an M48 BioRobot with a Quiagen Megatrack Kit.
Protocol Term Source REF	EFO	EFO	EFO
Protocol Software			
Term Source Name	The MGED Ontology	EFO	
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo	
SDRF File	E-GEOD-7621.sdrf.txt