Comment[ArrayExpressAccession]	E-GEOD-54619
MAGE-TAB Version	1.1		
Public Release Date	2014-02-03
Investigation Title	RNA-seq analysis of the transcriptomes of Piwi-deficient iPSCs		
Comment[Submitted Name]	RNA-seq analysis of the transcriptomes of Piwi-deficient iPSCs
Experiment Description	genome wide RNA-seq analysis of the transcriptomes of iPSCs that are derived from Miwi(-/-), Mili(-/-), and Miwi2(-/-) triple-knockout (TKO) mouse embryonic fibroblast Four biological replicates were used for the Piw triple knockout and control, respectively		
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	Lin	Lin	
Person First Name	Haifan	Haifan	
Person Email	haifan.lin@yale.edu		
Person Affiliation	Yale University		
Person Address	Yale University, 10 Amistad Street, New Haven, CT, USA		
Person Roles	submitter		
Protocol Name	P-GSE54619-3	P-GSE54619-2	P-GSE54619-1
Protocol Description	BWA aligner 0.7.5a w/ default parameters. Genome_build: mm9 Supplementary_files_format_and_content: mapped reads counts	Total RNA from individual iPS clones were isolated using the High Pure RNA Isolation Kit (Roche Diagnostics, Indianapolis, IN). For all samples, genomic DNA was digested with RNase-free DNase I. Library preparation were performed using the Illumina TruSeq RNA Sample Preparation kit. Samples were sequenced on an Illumina HiSeq 2000.	cells were grown in mouse ESC medium containing D-MEM with 15% fetal bovine serum (Gemini Bio-Products), 0.1 mM MEM Non-Essential Amino Acids (Life Technologies), 6 mM L-glutamine (Life Technologies) 0.1 mM 2-mercaptoethanol (Sigma), 1% Pen-Strep (Life Technologies) and 103Uml-1 of LIF (Millipore-ESGRO).
Protocol Type	normalization data transformation protocol	nucleic acid library construction protocol	growth protocol
Experimental Factor Name	GENOTYPE		
Experimental Factor Type	genotype		
Comment[SecondaryAccession]	GSE54619		
Comment[GEOReleaseDate]	2014-02-03		
Comment[ArrayExpressSubmissionDate]	2014-02-03		
Comment[GEOLastUpdateDate]	2014-04-09		
Comment[AEExperimentType]	RNA-seq of coding RNA		
Comment[AdditionalFile:Data1]	GSE54619_TriKO.txt		
Comment[SecondaryAccession]	SRP036148		
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR1156355-SRR1156362		
SDRF File	E-GEOD-54619.sdrf.txt