Comment[ArrayExpressAccession]	E-GEOD-42857
MAGE-TAB Version	1.1			
Public Release Date	2014-03-03
Investigation Title	Trancriptome study in rhesus monkey			
Comment[Submitted Name]	Trancriptome study in rhesus monkey
Experiment Description	While the next generation sequencing technology is accelerating the discovery of sites in RNA editing, the strategies to accurately identify the editome, the mechanism by which its profile is maintained and its functional significance remain controversial. Here, 90bp × 2, paired-end, strand-specific, polyA-postive RNA-Seq were performed in 3 rhesus monkey tissues, and 90bp × 2, paired-end, whole exome sequencing was performed in blood cells. Combining genome-wide identification and other quality control in multiple tissues from the same individual, we identified a list of editing sites in coding regions from the rhesus macaque, one of our closest evolutionary relatives. Low-scale verification validated all of these sites and the corresponding levels of editing. The editome in macaque coding region suggests RNA editing as a type of controlled, conserved regulation shaped by purifying selection. This submission represents RNA-Seq: cerebellum, lung, kidney and heart component of study.			
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	Li	Chen	
Person First Name	Jia-Yu	Chuan-Yun	Jia-Yu	
Person Email	jiayujiayu2008@163.com			
Person Affiliation	Peking University			
Person Address	Institute of Molecular Medicine, Peking University, No.5 Yiheyuan Road Haidian District, Beijing, China			
Person Roles	submitter			
Protocol Name	P-GSE42857-2	P-GSE42857-4	P-GSE42857-1	P-GSE42857-3
Protocol Description	RNA-Seq data were mapped to genome (rheMac2) tophat (v1.2.0) RPKM was calculated as previously described Genome_build: rheMac2 Supplementary_files_format_and_content: Table format. The gene and transcript ID, RPKM, reads number mapped to this gene, the length of exon and the position were listed in order.	raw reads were aligned by Tophat v1.2.0 only uniquely-mapped reads are retained RPKM values were calculated by in-house perl scripts Genome_build: rheMac2 Supplementary_files_format_and_content: RhesusBase1 Transcript ID, Ensembl Gene ID, RPKM Values, Number of Mapped Reads, Total Length of Exon, The Gene Locus	Trizol method Poly (A)-positive RNA was purified with the Dynabeads mRNA purification kit (Invitrogen) from 5μg of total RNA with high quality (RNA integrity number >7.5), following the manufacturer's instructions. A strand-specific RNA-Seq library preparation on the basis of the incorporation of deoxy-UTP was performed.	Total RNA was extracted from 2 rhesus monkey tissues using the Trizol method and analyzed by an Agilent 2100 bio-analyzer (Agilent Technologies). Poly (A)-positive RNA was purified with the Dynabeads mRNA purification kit (Invitrogen) from 5μg of total RNA with high quality (RNA integrity number >7.5), following the manufacturer's instructions. A strand-specific RNA-Seq library preparation on the basis of the incorporation of deoxy-UTP was performed.
Protocol Type	normalization data transformation protocol	normalization data transformation protocol	nucleic acid library construction protocol	nucleic acid library construction protocol
Experimental Factor Name	ORGANISM PART			
Experimental Factor Type	organism part			
Comment[SecondaryAccession]	GSE42857			
Comment[GEOReleaseDate]	2014-03-03			
Comment[ArrayExpressSubmissionDate]	2012-12-11			
Comment[GEOLastUpdateDate]	2014-03-18			
Comment[AEExperimentType]	RNA-seq of coding RNA			
Comment[SecondaryAccession]	SRP017517			
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR630492-SRR630494			
SDRF File	E-GEOD-42857.sdrf.txt