Biozentrum der Universität Basel and Swiss Institute of Bioinformatics (SIB)
2 ARTICLES PUBLISHED IN JoVE
Biology
PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
Markus Hafner 1, Markus Landthaler 2, Lukas Burger 3, Mohsen Khorshid 3, Jean Hausser 4, Philipp Berninger 4, Andrea Rothballer 1, Manuel Ascano 1, Anna-Carina Jungkamp 2, Mathias Munschauer 2, Alexander Ulrich 1, Greg S. Wardle 1, Scott Dewell 5, Mihaela Zavolan 3, Thomas Tuschl 1
1Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Rockefeller University, 2Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 3Biozentrum der Universität Basel and Swiss Institute of Bioinformatics (SIB), 4Biozentrum der Universität Basel and Swiss Institute of Bioinformatics (SIB), 5Genomics Resource Center, Rockefeller University
RNA transcripts are subject to extensive posttranscriptional regulation that is mediated by a multitude of trans-acting RNA-binding proteins (RBPs). Here we present a generalizable method to identify precisely and on a transcriptome-wide scale the RNA binding sites of RBPs.
Biology
3' End Sequencing Library Preparation with A-seq2
Georges Martin 1, Ralf Schmidt 1, Andreas J. Gruber 1, Souvik Ghosh 1, Walter Keller 1, Mihaela Zavolan 1,2
1Computational and Systems Biology, Biozentrum, University of Basel, 2Swiss Institute of Bioinformatics, Biozentrum, University of Basel
This protocol describes a method for mapping pre-mRNA 3' end processing sites.
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