Investigation Title	Transcription profiling of human lung cell lines A549, Beas-2B, and MeT5A exposed to asbestos, sampled at multiple time points							
Comment[Submitted Name]	Gene expression in asbestos exposed lung cells							
Experimental Design	time_series_design	in_vitro_design	cell_type_comparison_design	compound_treatment_design	co-expression_design	transcription profiling by array		
Experimental Design Term Source REF	mo		mo	mo	mo	EFO		
Comment[AEExperimentType]	transcription profiling by array							
Comment[AEExperimentDisplayName]	Transcription profiling by array of human lung cell lines A549, Beas-2B and MeT5A after treatment with asbestos over a time course							
Comment[ArrayExpressReleaseDate]	2007-11-08							
Comment[SecondaryAccession]	GSE6013							
Comment[AEMIAMESCORE]	5							
Comment[SecondaryAccession]	GDS2604							
Comment[ArrayExpressAccession]	E-GEOD-6013							
Comment[MAGETAB TimeStamp_Version]	2010-08-06 19:04:43 Last Changed Rev: 13058							
Experimental Factor Name	cell line	compound	time					
Experimental Factor Type	cell_line	compound	time					
Experimental Factor Term Source REF								
Person Last Name	Nymark							
Person First Name	Penny							
Person Mid Initials								
Person Email	penny.nymark@helsinki.fi							
Person Phone								
Person Fax								
Person Address	Pathology, Health and work ability, Finnish Institute of Occupational Health, Topeliuksenkatu 41aA, Helsinki, 00250, Finland							
Person Affiliation	Finnish Institute of Occupational Health							
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	2007-11-08							
PubMed ID	17331233							
Publication DOI	10.1186/1471-2164-8-62							
Publication Author List	Penny Nymark, Pamela M Lindholm, Mikko V Korpela, Leo Lahti, Salla Ruosaari, Samuel Kaski, Jaakko Hollmén, Sisko Anttila, Vuokko L Kinnula, Sakari Knuutila							
Publication Title	Gene expression profiles in asbestos-exposed epithelial and mesothelial lung cell lines.							
Publication Status	published							
Publication Status Term Source REF	EFO							
Experiment Description	Asbestos has been shown to cause chromosomal damage and DNA aberrations. The fiber is associated with many different lung diseases such as asbestosis, malignant mesothelioma, and lung cancer, but the disease-related processes are still largely unknown. Our aim was to identify specific gene expression profiles by using Affymetrix arrays, in human cell lines A549, Beas-2B, and MeT5A exposed to asbestos in a time-dependent manner. The hybridization data was analyzed using an algorithm specifically designed for clustering short time series expression data, a canonical correlation analysis (CCA) for identifying correlations between the cell lines, and a Gene Ontology (GO) analysis method for the identification of enriched differentially expressed biological processes. Samples from three cell lines were collected from asbestos exposed and non-exposed controls at 1h, 6h, 24h, 48h and 7 (168h) days (not all time-points for each cell lines). Replicates were done for one exposed sample of each cell line.							
Protocol Name	Affymetrix:Protocol:Hybridization-Unknown	P-AFFY-6						
Protocol Type	hybridization	feature_extraction						
Protocol Description	Title: Affymetrix Generic Hybridization. Description:	Title: Affymetrix CEL analysis. Description:						
Protocol Parameters								
Protocol Hardware								
Protocol Software	MicroArraySuite 5.0	MicroArraySuite 5.0						
Protocol Contact								
Protocol Term Source REF	mo							
SDRF File	E-GEOD-6013.sdrf.txt							
Term Source Name	mo	The MGED Ontology	ArrayExpress	NCI_thesaurus		mo	EFO	The MGED Ontology
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	ncithesaurus.obo.alt		http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/	http://mged.sourceforge.net/ontologies/MGEDontology.php
Term Source Version