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.

中文翻译：

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核糖体足迹分析文库中核酸酶介导的消耗偏差

核糖体足迹分析是一种基于高通量测序的技术，可提供活细胞翻译的详细和全局视图。这项技术的一个重要部分是去除不需要的、通常非常丰富的核糖体 RNA 序列，这些序列在文库中占主导地位并增加测序成本。最有效的商业解决方案 (Ribo-Zero) 已作为独立产品停产，市场上出现了许多新的、实验性独特的商业应用。在这里，我们评估了为人类样本的 RNA-seq 设计的几种市售替代品，发现它们通常不适合核糖体足迹分析。相反，我们建议使用定制设计的生物素化寡核苷酸，这些寡核苷酸在早期核糖体分析研究中被广泛使用。重要的，