Comment[ArrayExpressAccession]	E-GEOD-52530
MAGE-TAB Version	1.1			
Public Release Date	2013-12-02
Investigation Title	Global analyses of the effect of different cellular contexts on microRNA targeting (RNA-Seq)			
Comment[Submitted Name]	Global analyses of the effect of different cellular contexts on microRNA targeting (RNA-Seq)
Experiment Description	RNA-seqs followed by miRNA transfections (miR-124 and miR-155) into four different cell lines( HeLa, HEK293, Huh7, and IMR90). There are two biological replicates of RNA-seqs per each miRNA transfection per each sample and there are corresponding mock transfections.			
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	Nam	Nam	Rissland	Bartel
Person First Name	Jin-Wu	Jin-Wu	Olivia	David
Person Mid Initials				P
Person Email	coya75@gmail.com			
Person Affiliation	Hanyang University			
Person Address	Hanyang University, 222 Wangsimni Seongdong-gu, Seoul, South Korea			
Person Roles	submitter			
Protocol Name	P-GSE52530-3	P-GSE52530-1	P-GSE52530-2	
Protocol Description	Basecalls performed using CASAVA version 1.7 All RNA-seq data were mapped to the human reference genome (hg19) using Bowtie version 0.12.8 (Trapnell et al., 2009), allowing at most five genomic matches but choosing the best one (-n 1 -e 240 -m 5 --best --strata). To measure expression level, we estimated both reads per kilobases per million reads (RPKM) values and reads per million reads (RPM) values based on RefSeq annotation (Aug-22-2011 version). Quantile normalization was performed to reduce technical global bias of expressions between replicates and between wild type and transfected cells. Genome_build: hg19 Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for pUC19_1, pUC19_2, miR-124_1, miR-124_2, miR-155_1, and miR-155_2	Cells were transfected with Lipofectamine 2000 (Invitrogen) and 100 nM miRNA duplex or pUC19, as described by the manufacturer.	After 24 hours, cells were harvested, and RNA was extracted using TRI-reagent (Life Technologies). After RNA isolation, poly(A)+ RNA was selected using oligo(dT) beads (Invitrogen). RNA-seq libraries were prepared by either a ligation-based approach, as previously described (Guo et al., 2010), or a dUTP-based approach (Bioo Scientific), according the manufacturer’s directions.	
Protocol Type	normalization data transformation protocol	sample treatment protocol	nucleic acid library construction protocol	
Experimental Factor Name	CELL LINE	TRANSFECTION		
Experimental Factor Type	cell line	transfection		
Comment[SecondaryAccession]	GSE52530			
Comment[GEOReleaseDate]	2013-12-02			
Comment[ArrayExpressSubmissionDate]	2013-11-19			
Comment[GEOLastUpdateDate]	2014-01-14			
Comment[AEExperimentType]	RNA-seq of coding RNA			
Comment[AdditionalFile:Data1]	GSE52530_HEK293.expData.qn.txt			
Comment[AdditionalFile:Data2]	GSE52530_HEK293.expData.txt			
Comment[AdditionalFile:Data3]	GSE52530_HUH7.expData.qn.txt			
Comment[AdditionalFile:Data4]	GSE52530_HUH7.expData.txt			
Comment[AdditionalFile:Data5]	GSE52530_HeLa.expData.qn.txt			
Comment[AdditionalFile:Data6]	GSE52530_HeLa.expData.txt			
Comment[AdditionalFile:Data7]	GSE52530_IMR90.expData.qn.txt			
Comment[AdditionalFile:Data8]	GSE52530_IMR90.expData.txt			
Comment[SecondaryAccession]	SRP033131			
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR1032873-SRR1032896			
SDRF File	E-GEOD-52530.sdrf.txt