Comment[ArrayExpressAccession]	E-GEOD-55324
MAGE-TAB Version	1.1					
Public Release Date	2014-11-20
Investigation Title	Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates (HEK PAR-CLIP)					
Comment[Submitted Name]	Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates (HEK PAR-CLIP)
Experiment Description	Dicer is a deeply conserved endoribonuclease with key functions in small RNA biogenesis. Here we employed PAR-CLIP/iPAR-CLIP to identify direct Dicer binding sites in the transcriptomes of human cells and human. We found hundreds of novel miRNAs and non-canonical Dicer substrates with high sensitivity. Small RNA production depended on structure of the binding site and is globally biased towards the 5' arm of hairpins. Unexpectedly, in both species Dicer bound numerous hairpins inside mRNAs without observable small RNA production. Our data revealed ~100 mRNAs of protein coding genes to be targeted in both human and worm. These mRNAs significantly overlapped with the RNAi pathway. We also, unexpectedly, found that mitochondrial transcripts are Dicer targets in both species. We demonstrate functional consequences of Dicer binding by perturbation analysis. Taken together,we provide the first genome-wide catalog of direct Dicer targets. Our results suggest widespread function outside of miRNA biogenesis. PAR-CLIP basically as described previously (Hafner et al. 2010).					
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	Jens	Rybak-Wolf	Jens	Murakawa	Landthaler	Rajewsky
Person First Name	Marvin	Agnieszka	Marvin	Yasuhiro	Markus	Nikolaus
Person Email	marvin.jens@mdc-berlin.de					
Person Affiliation	Max Delbrueck Center for Molecular Medicine					
Person Phone	+493094062989					
Person Address	Systems Biology of Gene Regulatory Elements, Max Delbrueck Center for Molecular Medicine, Robert Rössle Str. 10 (H. 87), Berlin, Germany					
Person Roles	submitter					
Protocol Name	P-GSE55324-2	P-GSE55324-1				
Protocol Description	removal of default Illumina 3'adapter sequence with FLEXBAR (see supplementary methods) collapsing distinct read-sequences with custom script alignment with BOWTIE2 2.1.0 to hg19 cluster building and quality filtering to limit false-discovery rate with custom scripts Genome_build: hg19 Supplementary_files_format_and_content: GFF with genomic regions covered by filtered clusters (binding sites)	PAR-CLIP (Hafner et al. 2010) Illumina small RNA				
Protocol Type	normalization data transformation protocol	nucleic acid library construction protocol				
Publication Title	A Variety of Dicer Substrates in Human and C.�elegans.					
Publication Author List	Rybak-Wolf A, Jens M, Murakawa Y, Herzog M, Landthaler M, Rajewsky N					
PubMed ID	25416952					
Publication DOI	10.1016/j.cell.2014.10.040					
Comment[SecondaryAccession]	GSE55324					
Comment[GEOReleaseDate]	2014-11-20					
Comment[ArrayExpressSubmissionDate]	2014-02-25					
Comment[GEOLastUpdateDate]	2014-12-06					
Comment[AEExperimentType]	other					
Comment[AEExperimentType]	RNA-seq of non coding RNA					
Comment[AdditionalFile:Data1]	GSE55324_dicer1_4su_conservative.gff					
Comment[SecondaryAccession]	SRP038919					
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR1176638-SRR1176643					
SDRF File	E-GEOD-55324.sdrf.txt