Comment[ArrayExpressAccession]	E-GEOD-57043
MAGE-TAB Version	1.1			
Public Release Date	2014-04-25
Investigation Title	Dicer knockout NSCLC RNAseq and miRseq			
Comment[Submitted Name]	Dicer knockout NSCLC RNAseq and miRseq
Experiment Description	Dicer knockout NSCLC mRNAseq profiles the transcriptome, Dicer knockout NSCLC miRseq profiles the miRnome DicerHet and DicerKO NSCLC, 2 biological reps each genotype for mRNAseq, 1 biological rep each for miRseq			
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	Chen	Sharp	Chen	
Person First Name	Sidi	Phillip	Sidi	
Person Mid Initials		A		
Person Email	chensidi@mit.edu			
Person Affiliation	MIT			
Person Phone	7734144158			
Person Address	Biology, MIT, 77 Mass Ave, 76-461, Cambridge, MA, USA			
Person Roles	submitter			
Protocol Name	P-GSE57043-3	P-GSE57043-2	P-GSE57043-4	P-GSE57043-1
Protocol Description	adaptor clipping using fastxclipper of adaptors PE1.0 and PE2.0 discard reads shorter than 15bp mapping to mm9 transcriptome (mRNA-seq) or miRbase release 19 (miRseq) using tophat 1.3 calculation of gene expression level in fpkm using cufflinks 2.0.3 (mRNA-seq) calculation of gene expression level in rpm using custom scripts (miRseq) Genome_build: mm9 transcriptome, miRbase release 19 Supplementary_files_format_and_content: text files containing fpkm or rpm values for Dicer het and Dicer KO	Trizol-based total RNA extraction Illumina Tru-Seq mRNA sequencing library prep	Trizol-based total RNA extraction NEBNext small RNA library prep	Tumor-derived non-small cell lung cancer cells were cultured in DMEM with 10% FBS, passage 1:5 or 1:10 every 2~3 days in cell-culture dish
Protocol Type	normalization data transformation protocol	nucleic acid library construction protocol	nucleic acid library construction protocol	growth protocol
Experimental Factor Name	GENOTYPE			
Experimental Factor Type	genotype			
Publication Title	Global microRNA depletion suppresses tumor angiogenesis.			
Publication Author List	Chen S, Xue Y, Wu X, Le C, Bhutkar A, Bell EL, Zhang F, Langer R, Sharp PA			
PubMed ID	24788094			
Publication DOI	10.1101/gad.239681.114			
Comment[SecondaryAccession]	GSE57043			
Comment[GEOReleaseDate]	2014-04-25			
Comment[ArrayExpressSubmissionDate]	2014-04-24			
Comment[GEOLastUpdateDate]	2014-05-19			
Comment[AEExperimentType]	RNA-seq of coding RNA			
Comment[AEExperimentType]	RNA-seq of non coding RNA			
Comment[AdditionalFile:Data1]	GSE57043_dicerko_fpkm.txt			
Comment[AdditionalFile:Data2]	GSE57043_dicerko_hairpin_rpm.txt			
Comment[AdditionalFile:Data3]	GSE57043_dicerko_mature_rpm.txt			
Comment[SecondaryAccession]	SRP041414			
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR1260753-SRR1260758			
SDRF File	E-GEOD-57043.sdrf.txt