Nuclease-mediated depletion biases in ribosome footprint profiling libraries.

ABSTRACT: Ribosome footprint profiling is a high-throughput sequencing-based technique that provides detailed and global views of translation in living cells. An essential part of this technology is removal of unwanted, normally very abundant, ribosomal RNA sequences that dominate libraries and increase sequencing costs. The most effective commercial solution (Ribo-Zero) has been discontinued as a standalone product and a number of new, experimentally distinct commercial applications have emerged on the market. Here we evaluated several commercially available alternatives designed for RNA-seq of human samples and find them generally unsuitable for ribosome footprint profiling. We instead recommend the use of custom-designed biotinylated oligos, which were widely used in early ribosome profiling stud

SUBMITTER: Zinshteyn B 

PROVIDER: S-EPMC7491325 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature