Comment[ArrayExpressAccession]	E-MTAB-2687
Investigation Title	Integrin_a11_knockout					
Comment[Submitted Name]	Integrin_a11_knockout
Experimental Design	genetic_modification_design					
Comment[AEExperimentType]	transcription profiling by array					
Experimental Factor Name	genotype					
Experimental Factor Type	genotype					
Experimental Factor Term Source REF						
Person Last Name	Holdhus	Lu	Karlsen	Reed	Kusche-Gullberg	Gullberg
Person First Name	Rita	Ning	Tine	Rolf	Marion	Donald
Person Mid Initials			V.	K.		
Person Email	Rita.holdhus@mbi.uib.no	ning.lu@biomed.uib.no	tine.karlsen@biomed.uib.no	rolf.reed@biomed.uib.no	marion.kusche@biomed.uib.no	donald.gullberg@biomed.uib.no
Person Phone						
Person Address						
Person Affiliation	University of Bergen	Department of Biomedicine, University of Bergen, Norway, Centre for Cancer Biomarkers, Norwegian Centre of Excellence, University of Bergen, Norway	Department of Biomedicine, University of Bergen, Norway	Department of Biomedicine, University of Bergen, Norway, Centre for Cancer Biomarkers, Norwegian Centre of Excellence, University of Bergen, Norway	Department of Biomedicine, University of Bergen, Norway, Centre for Cancer Biomarkers, Norwegian Centre of Excellence, University of Bergen, Norway	Department of Biomedicine, University of Bergen, Norway, Centre for Cancer Biomarkers, Norwegian Centre of Excellence, University of Bergen, Norway
Person Roles	submitter	investigator	investigator	investigator	investigator	investigator
Person Roles Term Source REF	MO	MO	MO	MO	MO	MO
Quality Control Type	biological_replicates					
Quality Control Term Source REF	MO					
Replicate Type	biological_replicates					
Replicate Term Source REF	MO					
Date of Experiment	2012-10-15					
Public Release Date	2014-12-01					
PubMed ID						
Experiment Description	The project is to study how the expression of integrin alpha11beta1 on stromal cells (MEFs) affects the tumor cell behavior (A549 cells) in a heterospheroid co-culture model. We have found that the fibroblast alpha11beta1 integrin affects compaction and interstitial fluid pressure of the heterospheroids and regulates the migration and proliferation of A549 in the heterospheroids. We then performed the gene expression profiling of the A549 cells in the alpha11+/+/A549 and alpha11-/-/A549 heterospheroids. The Microarray analysis identified CXCL5 as one molecule down-regulated in A549 cells in the absence of alpha11 on the fibroblasts. Blocking CXCL5 function reduced cell proliferation and cell migration of A549 cells within spheroids.					
Protocol Name	P-MTAB-39850	P-TABM-4507	P-MTAB-39851	P-MTAB-39852	P-MTAB-39853	P-MTAB-39854
Protocol Type	SAMPLING	HYBRIDIZATION	SCANNING	EXTRACTION	DATA_PROCESSING	LABELING
Protocol Description	The RNA samples applied for Microarray were from the 6-day-old heterospheroids composed of SV40-immortalized mouse embryonic fibroblasts (MEFs), derived from wild-type (alpha11+/+) and Itga11 knock-out (alpha11-/-) mouse embryos at E14.5 as described as described in Popova et al. [1], and the lung adenocarcinoma cells A549 cells (purchased from ATCC). All the cells were cultured in Dulbeccos modified Eagles medium (DMEM) with Glutamax (Gibco) supplemented with 10% fetal bovine serum (FBS), 100 units/ml of penicillin and 0.1 mg/ml of streptomycin (all from PAA Laboratories). The heterospheroids (alpha11+/+/A549 and alpha11-/-/A549) were prepared with hanging-drop method as described in Osterholm et al. [2] with a ratio of MEFs: A549 = 4:1 and a total cell number 2.5x10^4/drop. All the heterospheroid samples were collected after 6 days culturing (10 spheroids/sample) and stored at -80oC before they were subjected to total RNA isolation. The total RNAs were isolated from the samples using RNeasy Mini Kit (Qiagen) according to the manufacturers instructions.	Whole-Genome Gene Expression Direct Hybridization Assay RevA - Hybridization protocol for Illumina	System guide for the iScan system and AutoLoader2. 11313539 Rev.A	The total RNAs were isolated from the samples using RNeasy Mini Kit (Qiagen) according to the manufacturerÍs instructions..	Illumina Bead Summary files were imported into the Genome Studio software for quality control and exported with control probes filtered out for import to J-Express 2009 analysis suite (www.molmine.com). AVG_Signal intensity values were quantile normalized and log 2 transformed.	The Illumina TotalPrep RNA Amplification Kit generates biotinylated, amplified RNA for hybridisation with Illumina Sentrix arrays. RNA is reversely transcribed by reverse transcriptase (RT) using an oligo(dT) primer bearing a T7 promoter. The resulting full-length cDNA then undergoes second strand synthesis and clean-up to become a template for in vitro transcription, biotin labelling and amplification with T7 RNA Polymerase.
Protocol Parameters						
Protocol Term Source REF	BASE	BASE	BASE	BASE	BASE	BASE
Term Source Name	ArrayExpress	MO	BASE
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://mged.sourceforge.net/ontologies/MGEDontology.php	mandelpil.ii.uib.no			
Term Source Version
SDRF File	E-MTAB-2687.sdrf.txt