The measurement of RNA abundance derived from massively parallel sequencing experiments is an essential technique. Methods that reduce ribosomal RNA levels are usually required prior to sequencing library construction because ribosomal RNA typically comprises the vast majority of a total RNA sample. For some experiments, ribosomal RNA depletion is favored over poly(A) selection because it offers a more inclusive representation of the transcriptome. However, methods to deplete ribosomal RNA are generally proprietary, complex, inefficient, applicable to only specific species, or compatible with only a narrow range of RNA input levels. Here, we describe Ribo-Pop (ribosomal RNA depletion for popular use), a simple workflow and antisense oligo design strategy that we demonstrate works over a wide input range and can be easily adapted to any organism with a sequenced genome. We provide a computational pipeline for probe selection, a streamlined 20-minute protocol, and ready-to-use oligo sequences for several organisms. We anticipate that our simple and generalizable "open source" design strategy would enable virtually any lab to pursue full transcriptome sequencing in their organism of interest with minimal time and resource investment.

中文翻译：

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Ribo-Pop：简单、经济且广泛适用的核糖体 RNA 去除

来自大规模平行测序实验的 RNA 丰度测量是一项必不可少的技术。在测序文库构建之前通常需要降低核糖体 RNA 水平的方法，因为核糖体 RNA 通常占总 RNA 样本的绝大多数。对于某些实验，核糖体 RNA 消耗优于 poly(A) 选择，因为它提供了更具包容性的转录组表示。然而，消耗核糖体 RNA 的方法通常是专有的、复杂的、低效的，仅适用于特定物种，或仅与窄范围的 RNA 输入水平兼容。在这里，我们描述了 Ribo-Pop（普遍使用的核糖体 RNA 消耗），我们展示了一个简单的工作流程和反义寡核苷酸设计策略，它适用于广泛的输入范围，并且可以轻松适应任何具有测序基因组的生物体。我们提供用于探针选择的计算管道、简化的 20 分钟协议以及适用于多种生物体的即用型寡核苷酸序列。我们预计，我们简单且可推广的“开源”设计策略将使几乎任何实验室都能以最少的时间和资源投入对其感兴趣的生物体进行完整的转录组测序。