Comment[ArrayExpressAccession]	E-GEOD-43507
MAGE-TAB Version	1.1					
Public Release Date	2013-05-01
Investigation Title	Genome-level Cell Responses to Digital Microfluidic Manipulation					
Comment[Submitted Name]	Genome-level Cell Responses to Digital Microfluidic Manipulation
Experiment Description	Analysis of mammalian cell responses to digital microfluidic manipulation. BA/F3 cells were manipulated on devices with 15 min continuous actuation at 400Vpp at 1 kHz or 18 kHz and compared to untreated control cells and cells heat shocked at 42C, 47C or 52C. Total RNA isolated from Ba/F3 murine cells, untreated or exposed to digital microfludic manipulation or heat shock.					
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	Au	Sam	Ryan	Aaron		
Person First Name	Sam	Au	Fobel	Wheeler		
Person Email	sam.au@utoronto.ca					
Person Affiliation	University of Toronto					
Person Address	University of Toronto, 160 College St. Room 440, Toronto, ON, Canada					
Person Roles	submitter					
Protocol Name	P-GSE43507-1	P-GSE43507-4	P-GSE43507-5	P-GSE43507-2	P-GSE43507-3	P-GSE43507-6
Protocol Description	Data analysis was conducted using Genespring v.11.5.1. Two batches of microarray data were normalized using the Empirical Bayes ComBat accommodation of batch effects using an R script. Each array batch contained 3 untreated control biological replicates for cross-batch normalization. Normalization by standard quantile method followed by a “per probe” median centered normalization ID_REF =  VALUE = Cross-Batch normalized. Quantile Normalized.	RNA samples were labelled using Illumina TotalPrep-96 RNA Amplification Kit Lot #1108030 Ambion as per protocol. 1.5 ng cRNA randomized and hybridized	Standard Illumina hybridization protocol	Cells were either untreated (negative), heat shocked for 15 minutes at 42C, 47C or 52C or actuated continuously on device for 15 minutes at 400Vpp and either 1 kHz or 18 kHz sinusoidal frequencies	Cells were lysed and total RNA extracted and purified using Arcturus Picopure RNA Isolation kits (Applied Biosystems) according to manufacturer protocols. Quality control by Agilent Bioanalyzer	Standard Illumina scan protocol
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	TREATMENT					
Experimental Factor Type	treatment					
Comment[SecondaryAccession]	GSE43507					
Comment[GEOReleaseDate]	2013-05-01					
Comment[ArrayExpressSubmissionDate]	2013-01-15					
Comment[GEOLastUpdateDate]	2013-05-02					
Comment[AEExperimentType]	transcription profiling by array					
Comment[AdditionalFile:Data1]	GSE43507.txt					
Comment[AdditionalFile:Data2]	GSE43507_BatchA_sample_probe.txt					
Comment[AdditionalFile:Data3]	GSE43507_BatchB_sample_probe.txt					
Comment[AdditionalFile:Data4]	GSE43507_non-normalized.txt					
SDRF File	E-GEOD-43507.sdrf.txt