期刊
RNA
卷 26, 期 10, 页码 1481-1488出版社
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1261/rna.075523.120
关键词
RNA-seq; Ribo-Zero; rRNA depletion; ribo-seq; ribosome profiling
资金
- National Institutes of Health, National Institute of General Medical Sciences [2R37GM059425-14, 5K99GM135450-02]
- Howard Hughes Medical Institute (HHMI)
- Cystic Fibrosis Foundation [GREEN16G0]
- Damon Runyon Cancer Research Foundation [DRG-2250-16]
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 studies. Importantly, we warn that depletion solutions based on targeted nuclease cleavage significantly perturb the high-resolution information that can be derived from the data, and thus do not recommend their use for any applications that require precise determination of the ends of RNA fragments.
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