Comment[ArrayExpressAccession]	E-GEOD-40383
MAGE-TAB Version	1.1						
Public Release Date	2013-07-20
Investigation Title	Prostate cancer cell lines: non-targeting siRNA versus SChLAP1-siRNA treated						
Comment[Submitted Name]	Prostate cancer cell lines: non-targeting siRNA versus SChLAP1-siRNA treated
Experiment Description	SChLAP1 is a novel long non-coding RNA expressed in prostate cancer. Here we performed transcriptional profiling of the prostate cancer cell lines LNCaP and 22Rv1 comparing non-targeting siRNA treatment versus SChLAP1-siRNA treatment. Goal was to determine the effect of SChLAP1 knockdown on gene expression in prostate cancer. Two-condition experiment: non-targeting siRNA versus SChLAP1 siRNA treated cells. Biological replicates: 1 control replicate, 2 treatment replicates.  Technical replicates: 3 replicates per SChLAP1 siRNA.  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	Xiaojung	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-GSE40383-1	P-GSE40383-5	P-GSE40383-6	P-GSE40383-2	P-GSE40383-3	P-GSE40383-4	P-GSE40383-7
Protocol Description	Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Control Features were omitted. The LogRatio and PValueLogRatio columns from each feature file were then merged into a single processed data matrix ID_REF =  VALUE = 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	TRANSFECTED WITH					
Experimental Factor Type	cell line	transfected with					
Comment[SecondaryAccession]	GSE40383						
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-40383.sdrf.txt