Comment[ArrayExpressAccession]	E-GEOD-51619
MAGE-TAB Version	1.1			
Public Release Date	2013-10-28
Investigation Title	Evaluation of TRAP-sequencing technology with a versatile conditional mouse model			
Comment[Submitted Name]	Evaluation of TRAP-sequencing technology with a versatile conditional mouse model
Experiment Description	Evaluation of TRAP-sequencing by comparing transcriptomes and translatomes of different organs and distinct cell populations. E14.5 brain and kidney transcriptome and translatome profiling of organs or distinct cell populations from these organs was performed using the Illumina TruSeq RNA technology.			
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	Stenman	Hupe	Li	Stenman
Person First Name	Jan	Mike	Minerva	Jan
Person Mid Initials	M		X	M
Person Email	jan.stenman@licr.ki.se			
Person Affiliation	Ludwig Institute for Cancer Research Ltd			
Person Address	Ludwig Institute for Cancer Research Ltd, Box 240, Solna, Sweden			
Person Roles	submitter			
Protocol Name	P-GSE51619-2	P-GSE51619-3	P-GSE51619-1	
Protocol Description	All reads were aligned to the mouse (mm10) genome using RNA-Seq unified mapper (RUM; Grant et al., 2011). Non-uniquely mapped reads were removed. Rpkgforgenes (available at http:sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -bamu, was used to generate RPKM values and read counts. Gene annotiations used were transcripts in RefSeq (January 2013). Genome_build: UCSC version mm10 (Genome Reference Consortium GRCm38) Supplementary_files_format_and_content: Gene expression values and read counts (tab-delimited text file).	Organ was dissected and homogenized in TRAP lysis buffer (Heiman et al., 2008, Cell). Extract was cleared by centrifugation. Ribosome-bound RNA was immunoprecipitated. RNA was eluted and purified using RNeasy® Micro Kit (Qiagen). TruSeq RNA Sample Preparation Kits v2	Organ was dissected and homogenized in TRAP lysis buffer (Heiman et al., 2008, Cell). Extract was cleared by centrifugation. RNA was purified using RNeasy® Micro Kit (Qiagen). TruSeq RNA Sample Preparation Kits v2	
Protocol Type	normalization data transformation protocol	nucleic acid library construction protocol	nucleic acid library construction protocol	
Experimental Factor Name	CELL TYPE	GENOTYPE	ORGANISM PART	
Experimental Factor Type	cell type	genotype	organism part	
Publication Title	Evaluation of TRAP-sequencing technology with a versatile conditional mouse model.			
Publication Author List	Hupe M, Li MX, Gertow Gillner K, Adams RH, Stenman JM			
PubMed ID	24165879			
Publication DOI	10.1093/nar/gkt995			
Comment[SecondaryAccession]	GSE51619			
Comment[GEOReleaseDate]	2013-10-28			
Comment[ArrayExpressSubmissionDate]	2013-10-23			
Comment[GEOLastUpdateDate]	2013-11-15			
Comment[AEExperimentType]	RNA-seq of coding RNA			
Comment[SecondaryAccession]	SRP031883			
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR1015935-SRR1015955			
SDRF File	E-GEOD-51619.sdrf.txt