The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis.

ABSTRACT: Ribosome profiling is a technique that permits genome-wide, quantitative analysis of translation and has found broad application in recent years. Here we describe a modified profiling protocol and software package designed to benefit more broadly the translation community in terms of simplicity and utility. The protocol, applicable to diverse organisms, including organelles, is based largely on previously published profiling methodologies, but uses duplex-specific nuclease (DSN) as a convenient, species-independent way to reduce rRNA contamination. We show that DSN-based depletion compares favorably with other commonly used rRNA depletion strategies and introduces little bias. The profiling protocol typically produces high levels of triplet periodicity, facilitating the detection of coding

SUBMITTER: Chung BY 

PROVIDER: S-EPMC4574750 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature