Comment[ArrayExpressAccession]	E-GEOD-40384
MAGE-TAB Version	1.1						
Public Release Date	2013-07-20
Investigation Title	siRNA Knockdown of SWI/SNF complex proteins in prostate cancer cell lines						
Comment[Submitted Name]	siRNA Knockdown of SWI/SNF complex proteins in prostate cancer cell lines
Experiment Description	Here we performed transcriptional profiling of the prostate cancer cell lines LNCaP and 22Rv1 comparing non-targeting siRNA treatment versus siRNAs targeting SWI/SNF complex proteins (SMARCA2, SMARCA4, and SMARCB1). Goal was to determine the effect of SWI/SNF knockdown on gene expression in prostate cancer. Two-condition experiment: non-targeting siRNA versus SWI/SNF-siRNA treated cells. Three SWI/SNF proteins were targeted: SMARCA2, SMARCA4, and SMARB1. Biological replicates: 1 control replicate, 2 treatment replicates per SWI/SNF protein.  Technical replicates: 1 replicate per SWI/SNF protein. Cell lines: 22Rv1 and LNCaP.						
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	Iyer	Jing	Iyer	Prensner			
Person First Name	Matthew	Xiaojun	Matthew	John			
Person Mid Initials			K	R			
Person Email	mkiyer@med.umich.edu						
Person Affiliation	University of Michigan						
Person Phone	7346154503						
Person Address	Michigan Center for Translational Pathology, University of Michigan, 5316 CCGC 0940 1400 E. Medical Center Drive, Ann Arbor, MI, USA						
Person Roles	submitter						
Protocol Name	P-GSE40384-1	P-GSE40384-5	P-GSE40384-6	P-GSE40384-2	P-GSE40384-3	P-GSE40384-4	P-GSE40384-7
Protocol Description	Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Control features were removed. A merged processed data file was created by aggregating the logFoldChange and PValueLogFoldChange columns from each of the feature files ID_REF =  VALUE = normalized log2 ratio representing test/reference Detection Pval = 	10 M-5g of total RNA were primed with 2 M-5l of 100 M-5M T16N2 DNA primer at 70M-0C for 10 min, then reversed transcribed at 42M-0C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 M-5M each dATP, dTTP, dGTP, with 25 M-5M dCTP, 25 M-5M Cy3-label	Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential	Cells were plated in 100mM plates at a desired concentration and transfected with 20uM experimental siRNA oligos or non-targeting controls twice, at 12 hours and 36 hours post-plating. Knockdowns were performed with Oligofectamine and Optimem. Knockdown efficiency was determined by qPCR.	Cells were grown in RPMI 1640 (Invitrogen) and supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin.	Total RNA was isolated using Trizol and an RNeasy Kit (Invitrogen) with DNase I digestion according to the manufacturerM-bM-^@M-^Ys instructions.	Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	CELL LINE	SIRNA SEQUENCE	TRANSFECTED WITH				
Experimental Factor Type	cell line	sirna sequence	transfected with				
Comment[SecondaryAccession]	GSE40384						
Comment[GEOReleaseDate]	2013-07-20						
Comment[ArrayExpressSubmissionDate]	2012-08-27						
Comment[GEOLastUpdateDate]	2013-07-21						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-40384.sdrf.txt