Investigation Title	Transcription profiling of human post mortem spinal cord grey matter from sporadic and familial ALS patients vs controls to identify amyotrophic lateral sclerosis (ALS) associated genes	
Comment[Submitted Name]	Amyotrophic lateral sclerosis	
Experimental Design	disease_state_design	co-expression_design	transcription profiling by array	
Experimental Design Term Source REF	mo	mo	EFO	
Comment[ArrayExpressReleaseDate]	2007-09-26	
Comment[SecondaryAccession]	GSE833	
Comment[AEMIAMESCORE]	4	
Comment[SecondaryAccession]	GDS412	
Comment[ArrayExpressAccession]	E-GEOD-833	
Comment[MAGETAB TimeStamp_Version]	2010-08-08 00:41:10 Last Changed Rev: 13058	
Experimental Factor Name	DiseaseState	
Experimental Factor Type	disease_state	
Experimental Factor Term Source REF	
Person Last Name	Dangond	
Person First Name	Fernando	
Person Mid Initials	
Person Email	fdangond@rics.bwh.harvard.edu	
Person Phone	
Person Fax	
Person Address	Brigham and Women's Hospital Laboratories, Cambridge, 02139, USA	
Person Affiliation	Brigham and Women's Hospital Laboratories	
Person Roles	submitter	
Person Roles Term Source REF		
Quality Control Type	
Quality Control Term Source REF	
Replicate Type	
Replicate Term Source REF	
Normalization Type	
Normalization Term Source REF	
Date of Experiment	
Public Release Date	2007-09-26	
PubMed ID	14645737	
Publication DOI	14645737	
Publication Author List	Fernando Dangond, Daehee Hwang, Sandra Camelo, Piera Pasinelli, Matthew P Frosch, Gregory Stephanopoulos, George Stephanopoulos, Robert H Brown, Steven R Gullans	
Publication Title	Molecular signature of late-stage human ALS revealed by expression profiling of postmortem spinal cord gray matter.	
Publication Status	journal_article	
Publication Status Term Source REF	The MGED Ontology	
Experiment Description	Identification of amyotrophic lateral sclerosis (ALS) associated genes. Post mortem spinal cord grey matter from sporadic and familial ALS patients compared with controls.	
Protocol Name	P-G833-1	P-G833-2	P-G833-3	
Protocol Type	specified_biomaterial_action	hybridization	feature_extraction	
Protocol Description	All samples were obtained from local or national tissue banks and were processed under full compliance with Institutional Review Board requirements. For DNA microarray analysis, total RNA was obtained from postmortem gray matter of lumbar spinal cord from 11 individuals including 7 with ALS and 4 normal controls. The seven ALS spinal cords were obtained from five individuals with sporadic ALS (SALS) and two with familial ALS (FALS). Of the two familial specimens, one was from an individual with a superoxide dismutase 1 mutation (SOD1-A4V); the gene defect in the other was not defined (samples were not tested for the recently described Alsin mutations since the phenotype did not correspond to that described for familial juvenile ALS). The average age of death recorded for the study subjects was 56 yr for ALS and 60.5 yr for the non-ALS samples. Most ALS samples were subjected to histopathological examination prior to inclusion in the study. Findings included loss of anterior horn cells or chromatolysis accompanied by corticospinal tract degeneration. Recorded tissue collection times ranged from 2-18 h postmortem, with the averages being 10 h for ALS and 10 h for normals.	The hybridization mixture was heated to 99°C for 5 min, spun, and incubated at 45°C for 5 min, then injected into the probe array cartridge. Hybridizations were carried out at 45°C for 16 h with mixing at 60 rpm.	Following washes, probe arrays were scanned twice at 6 µm resolution using the GeneChip system confocal scanner. All samples were hybridized to Test1 or Test2 microarrays to assess cRNA quality control, prior to hybridization to HuGeneFL arrays.	
Protocol Parameters	
Protocol Hardware	
Protocol Software	
Protocol Contact	
Protocol Term Source REF			The MGED Ontology	
SDRF File	E-GEOD-833.sdrf.txt	
Term Source Name	ncbitax		NCI_thesaurus	The MGED Ontology	ArrayExpress	mo	EFO	The MGED Ontology	
Term Source File	http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html		ncithesaurus.obo.alt	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/	http://mged.sourceforge.net/ontologies/MGEDontology.php	
Term Source Version