Comment[ArrayExpressAccession]	E-GEOD-43097
MAGE-TAB Version	1.1					
Public Release Date	2014-05-02
Investigation Title	Integrin α3b1-dependent gene expression in MDA-MB-231 breast  cancer cells					
Comment[Submitted Name]	Integrin α3b1-dependent gene expression in MDA-MB-231 breast  cancer cells
Experiment Description	Gene-level and exon-level analysis of gene expression in MDA-MB-231 cells that stably express control shRNA or integrin α3-targeting shRNA. The laminin-332-binding integrin α3b1 is expressed highly in many breast cancer cells, but its roles in regulating gene expression programs that promote breast cancer progression have not been explored.  In order to identify genes that are regulated by α3b1 in human breast cancer cells, we used a lentiviral approach to express an α3-targeting shRNA to suppress integrin α3b1 in MDA-MB-231 cells, and we identified subsequent changes in gene expression and alternate exon useage. We used the Affymetrix Human Exon 1.0 ST platform to analyze biological replicates of MDA-MB-231 cells that were transduced with lentivirus to stably express either control shRNA or α3-targeting shRNA.  Array data was processed by Affymetrix Exon Array Computational Tool.					
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl				
Person Last Name	Chittur	DiPersio	Subbaram	Chittur		
Person First Name	Sridar	C	Sita	Sridar		
Person Mid Initials		M		V		
Person Email	schittur@albany.edu					
Person Affiliation	SUNY-University at Albany					
Person Phone	518-591-7215					
Person Address	Center for Functional Genomics, SUNY-University at Albany, One Discovery Drive, CRC 342G, Rensselaer, NY, USA					
Person Roles	submitter					
Protocol Name	P-GSE43097-1	P-GSE43097-4	P-GSE43097-5	P-GSE43097-2	P-GSE43097-3	P-GSE43097-6
Protocol Description	CHP files generated at both gene- and exon-level with Affymetrix Expression Console using Core probeset ID_REF =  VALUE = Quantification	Standard Affymetrix WT protocol starting with 1ug total RNA and incuding riboreduction	Standard Affymetrix WT protocol	MDA-MB-231 cells with stable expression of either control shRNA or α3-targeting shRNA were maintained at 37 degrees C, 5% CO2, on standard tissue culture plates. Cells were grown in DMEM supplemented with 10% FBS 100 units/ml penicillin and 100 μg/ml streptomycin.	Total cellular RNA was isolated from cells using the RNeasy Plus isolation kit (Qiagen, Valencia, CA), and quality was confirmed on an Agilent Bioanalyzer.	Standard Affymetrix rotocol for GCS30007G scanner
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	GENOTYPE					
Experimental Factor Type	genotype					
PubMed ID	24434582					
Comment[SecondaryAccession]	GSE43097					
Comment[GEOReleaseDate]	2014-05-02					
Comment[ArrayExpressSubmissionDate]	2012-12-21					
Comment[GEOLastUpdateDate]	2014-05-02					
Comment[AEExperimentType]	transcription profiling by array					
Comment[AdditionalFile:Data1]	GSE43097_MD_1_MBA231_con1.CEL					
Comment[AdditionalFile:Data2]	GSE43097_MD_2_MBA231_con2.CEL					
Comment[AdditionalFile:Data3]	GSE43097_MD_3_MBA231_alpha3_kd1.CEL					
Comment[AdditionalFile:Data4]	GSE43097_MD_4_MBA231_alpha3_kd2.CEL					
SDRF File	E-GEOD-43097.sdrf.txt