Transcriptomics

Dataset Information

363

3' isoform specific RNA IP (3' isRIP-seq) for PUF3 RBP in budding yeast


ABSTRACT: Exponentially growing cells (OD 0.5-0.8) from the TAP-tagged strain were harvested by ultracentrifugation followed by of washing and flash freezing in liquid nitrogen and breakage in FastPrep24 (ZYmoresearch S6005). The lysate was subjected to IP with Dyna M280 sheep anti rabbit IgG beads for 2h at 4C. An aliquot was taken before the IP as an input control. The IP of the RNA-protein complex was subjected to cleavage by TEV protease to cleave the TAP-tag off the protein. The bound RNA was then precipitated in phenol/chloroform/isoamyl-alcohol and sequenced using 3' T-filling protocol as described by Wilkening et al 2013 to obtain accurate quantification of 3' isoforms. We used the R Bioconductor package DESeq2 (Anders and Huber 2010) to call for differential log change between the Input and the RNA-IP sample and took all those isoforms as differentially regulated which had more than 4-fold change at a FDR of 10% as reported by the package.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Saccharomyces cerevisiae  

SUBMITTER: Gupta Ishaan  

PROVIDER: E-MTAB-2103 | ArrayExpress | 2014-11-13

SECONDARY ACCESSION(S): ERP004367

REPOSITORIES: ArrayExpress, ENA

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Publications

Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions.

Gupta Ishaan I   Clauder-Münster Sandra S   Klaus Bernd B   Järvelin Aino I AI   Aiyar Raeka S RS   Benes Vladimir V   Wilkening Stefan S   Huber Wolfgang W   Pelechano Vicent V   Steinmetz Lars M LM  

Molecular systems biology 20140225


Recent research has uncovered extensive variability in the boundaries of transcript isoforms, yet the functional consequences of this variation remain largely unexplored. Here, we systematically discriminate between the molecular phenotypes of overlapping coding and non-coding transcriptional events from each genic locus using a novel genome-wide, nucleotide-resolution technique to quantify the half-lives of 3' transcript isoforms in yeast. Our results reveal widespread differences in stability  ...[more]

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