Investigation Title	Transcription profiling of mouse SPARC-null vs. wild-type lens epithelium	
Comment[Submitted Name]	SPARC-null vs. wild-type lens epithelium	
Experimental Design	unknown_experiment_design_type	transcription profiling by array	
Experimental Design Term Source REF		EFO	
Comment[SecondaryAccession]	GSE13402	
Comment[ArrayExpressReleaseDate]	2009-05-11	
Comment[AEMIAMESCORE]	3	
Comment[ArrayExpressAccession]	E-GEOD-13402	
Comment[MAGETAB TimeStamp_Version]	2010-07-30 09:56:46 Last Changed Rev: 13058	
Experimental Factor Name	
Experimental Factor Type	
Experimental Factor Term Source REF	
Person Last Name	Greiling	
Person First Name	Teri	
Person Mid Initials	
Person Email	teri@u.washington.edu	
Person Phone	
Person Fax	
Person Address	John I. Clark, Biological Structure, University of Washington, Box 357420, Seattle, 98195-7420, USA	
Person Affiliation	University of Washington	
Person Roles	submitter	
Person Roles Term Source REF	The MGED Ontology	
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	2009-05-11	
PubMed ID	
Publication DOI	
Publication Author List	
Publication Title	
Publication Status	
Publication Status Term Source REF	
Experiment Description	SPARC is a matricellular glycoprotein involved in regulation of the extracellular matrix, growth factors, adhesion, and migration.  SPARC-null mice have altered basement membranes and develop posterior sub-capsular cataracts with cell swelling and equatorial vacuoles.  Exchange of fluid, nutrients, and waste products in the avascular lens is driven by a unique circulating ion current.  Here we demonstrate that SPARC-null mouse lenses exhibit abnormal circulation of fluid, ion, and small molecules which leads to altered fluorescein distribution in vivo, loss of resting membrane polarization, and altered distribution of small molecules.  Microarray analysis of SPARC-null lenses showed changes in gene expression of ion channels and receptors, matrix and adhesion genes, cytoskeleton, immune response genes, and cell signaling molecules.  Our results demonstrate that the regulation of SPARC on cell-capsular matrix interactions can influence the circulation of fluid and ions in the lens, and the phenotype in the SPARC-null mouse lens is the result of multiple intersecting pathways. Experiment Overall Design: Lens epithelial cells from 7 lenses of littermate mice were isolated by laser capture microdissection.  3 wild-type lenses from 3 different mice and 4 knock-out lenses from 3 different mice were used as biological replicates.	
Protocol Name	P-G13402-1	P-G13402-2	P-G13402-4	P-G13402-3	P-AFFY-6	Affymetrix:Protocol:ExpressionStat	
Protocol Type	grow	specified_biomaterial_action	nucleic_acid_extraction	labeling	feature_extraction	bioassay_data_transformation	
Protocol Description	Normal housing	Lens was cryosectioned, stained with Cressyl Violet, and dehydrated. Laser capture microdissection (Arcturus PixCell2e) was used to remove epithelial cells from each section.	RNeasy micro kit (Qiagen)	Two cycle amplification using Ambion MessageAmp II aRNA amplification kit and MessageAmp II-biotin enhanced amplification kits	Title: Affymetrix CEL analysis. Description: 	Title: Affymetrix CHP Analysis (ExpressionStat). Description: 	
Protocol Parameters	
Protocol Hardware	
Protocol Software					MicroArraySuite 5.0	MicroArraySuite 5.0	
Protocol Contact	
Protocol Term Source REF						The MGED Ontology	
SDRF File	E-GEOD-13402.sdrf.txt	
Term Source Name	NCBI Taxonomy		The MGED Ontology	ArrayExpress	EFO	The MGED Ontology	
Term Source File	http://www.ncbi.nlm.nih.gov/Taxonomy/		http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	http://www.ebi.ac.uk/efo/	http://mged.sourceforge.net/ontologies/MGEDontology.php	
Term Source Version