Comment[ArrayExpressAccession]	E-GEOD-56435
MAGE-TAB Version	1.1			
Public Release Date	2014-07-24
Investigation Title	Genome-wide mapping of yeast RNA polymerase II termination			
Comment[Submitted Name]	Genome-wide mapping of yeast RNA polymerase II termination
Experiment Description	Using a modification of the yeast anchor away and PAR-CLIP protocols, we have mapped the position of Pol II genome-wide in living yeast cells after depletion of components of either the polyadenylation (pA) or non-pA termination complexes. Depletion of Ysh1 from the nucleus does not lead to readthrough transcription. In contrast, depletion of the termination factor Nrd1 leads to widespread runaway elongation of non-pA transcripts. Depletion of Sen1 also leads to readthrough at non-pA terminators but in contrast to Nrd1 this readthrough appears less processive. Examination of PAR-CLIP sequencing data of Pol II after removal of different transcriptional termination factors.			
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	Corden	Schaughency	Corden	Merran
Person First Name	Jeff	Paul	Jeffry	Jonathan
Person Email	jcorden@jhmi.edu			
Person Affiliation	JHU			
Person Address	Molecular Bio and Gen, JHU, 725 N Wolfe Street, Baltimore, MD, USA			
Person Roles	submitter			
Protocol Name	P-GSE56435-2	P-GSE56435-1		
Protocol Description	Trimmed: 3' Adaptor using R/BioConductor Package. Filtered: Reads greater than 13 nucleotides. Script available upon request. Condensed: Identical sequences into 1 unique read. Script available upon request. Aligned: All reads to a genome only consisting of the tRNA genes of the yeast SacCer3 (R64) genome using Bowtie 1.0. Aligned: All reads that did not align to the tRNA yeast genome to the SacCer3 (R64) genome using Bowtie 1.0. Genome_build: R64-1-1 Supplementary_files_format_and_content: Wig files	PAR-CLIP Adaptation of NEB-Next Small RNA Library Prep Set for Illumina (Multiplex version).		
Protocol Type	normalization data transformation protocol	nucleic acid library construction protocol		
Experimental Factor Name	STRAIN/BACKGROUND	MAXIMUM TIME OF RAPAMYCIN EXPOSURE		
Experimental Factor Type	strain/background	maximum time of rapamycin exposure		
Comment[SecondaryAccession]	GSE56435			
Comment[GEOReleaseDate]	2014-07-24			
Comment[ArrayExpressSubmissionDate]	2014-04-01			
Comment[GEOLastUpdateDate]	2014-07-26			
Comment[AEExperimentType]	RNA-seq of coding RNA			
Comment[SecondaryAccession]	SRP040778			
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR1212399-SRR1212407			
SDRF File	E-GEOD-56435.sdrf.txt