Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD 21702, USA.
Nucleic Acids Res. 2021 Jan 8;49(D1):D871-D876. doi: 10.1093/nar/gkaa848.
With the technology's accessibility and ease of use, CRISPR has been employed widely in many different organisms and experimental settings. As a result, thousands of publications have used CRISPR to make specific genetic perturbations, establishing in itself a resource of validated guide RNA sequences. While numerous computational tools to assist in the design and identification of candidate guide RNAs exist, these are still just at best predictions and generally, researchers inevitably will test multiple sequences for functional activity. Here, we present dbGuide (https://sgrnascorer.cancer.gov/dbguide), a database of functionally validated guide RNA sequences for CRISPR/Cas9-based knockout in human and mouse. Our database not only contains computationally determined candidate guide RNA sequences, but of even greater value, over 4000 sequences which have been functionally validated either through direct amplicon sequencing or manual curation of literature from over 1000 publications. Finally, our established framework will allow for continual addition of newly published and experimentally validated guide RNA sequences for CRISPR/Cas9-based knockout as well as incorporation of sequences from different gene editing systems, additional species and other types of site-specific functionalities such as base editing, gene activation, repression and epigenetic modification.
随着技术的普及和易用性，CRISPR 已经被广泛应用于许多不同的生物体和实验环境中。因此，数以千计的出版物已经使用 CRISPR 来进行特定的基因干扰，从而本身就建立了一个经过验证的向导 RNA 序列资源。虽然有许多用于辅助设计和识别候选向导 RNA 的计算工具，但这些仍然只是最好的预测，通常，研究人员不可避免地会测试多个序列的功能活性。在这里，我们介绍 dbGuide（https://sgrnascorer.cancer.gov/dbguide），这是一个用于人类和小鼠基于 CRISPR/Cas9 的基因敲除的功能验证向导 RNA 序列数据库。我们的数据库不仅包含计算确定的候选向导 RNA 序列，而且更有价值的是，超过 4000 个序列已经通过直接扩增子测序或从超过 1000 篇文献的手动整理进行了功能验证。最后，我们建立的框架将允许不断添加新发布的和经过实验验证的基于 CRISPR/Cas9 的基因敲除向导 RNA 序列，并纳入来自不同基因编辑系统、其他物种和其他类型的特定于位置的功能，如碱基编辑、基因激活、抑制和表观遗传修饰的序列。
