Comment[ArrayExpressAccession]	E-GEOD-44336
MAGE-TAB Version	1.1			
Public Release Date	2013-02-19
Investigation Title	Degradome sequencing reveals an endogenous microRNA target in C. elegans			
Comment[Submitted Name]	Degradome sequencing reveals an endogenous microRNA target in C. elegans
Experiment Description	Total poly(A) RNAs from wild-type adult stage worms were subjected to high-throughput sequencing using an Illumina platform to detect RNA cleavage fragment. Wild-type (N2) C. elegans			
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	Shin	Park	Nam	Shin
Person First Name	Chanseok	June	Jin	Chanseok
Person Mid Initials		H	W	
Person Email	cshin@snu.ac.kr			
Person Affiliation	Seoul National University			
Person Address	Seoul National University, Gwanak-gu Daehak-dong, SEOUL, South Korea			
Person Roles	submitter			
Protocol Name	P-GSE44336-1	P-GSE44336-2		
Protocol Description	Worms were harvested at the appropriate stage, washed twice with M9 buffer, and frozen in liquid nitrogen. Total RNA was extracted using Tri-Reagent (Ambion), which was further purified with phenol:chloroform followed by precipitation with ethanol. Poly(A) RNA was enriched from wild-type adult C. elegans total RNA using the Oligotex mRNA kit (QIAGEN). A custom 5' RNA adapter containing a MmeI recognition site was ligated to the poly(A) RNA possessing a 5'-monophosphate, by T4 RNA ligase, and the ligated products were reverse transcribed. This cDNA was amplified and then digested with restriction enzyme MmeI, which cleaves 20 nts 3’ of the recognition site. This MmeI digested product was ligated to a 3’ double strand adaptor, amplified by PCR, gel-purified and submitted for Illumina sequencing.	7.6 million of 20-nt tags from wild-type adult cleavage libraries were mapped to the C. elegans genome (ce6), requiring a perfect match. For tags mapped to at most 10 genomic loci, the final tag number was normalized with the loci number. Of genome-mapping tags, ~70% mapped to exons of annotated genes (RefSeq with new 3′UTR annotations), including rRNAs, ~25% mapped to intergenic regions, ~3% mapped to intronic regions of genes, and 0.5% mapped antisense to annotated genes. Genome_build: C. elegans genome (ce6)		
Protocol Type	nucleic acid library construction protocol	feature_extraction		
Comment[SecondaryAccession]	GSE44336			
Comment[GEOReleaseDate]	2013-02-19			
Comment[ArrayExpressSubmissionDate]	2013-02-14			
Comment[GEOLastUpdateDate]	2013-02-22			
Comment[AEExperimentType]	RNA-seq of coding RNA			
Comment[SecondaryAccession]	SRP018765			
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR748237-SRR748239			
SDRF File	E-GEOD-44336.sdrf.txt