Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA.
Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA.
Nucleic Acids Res. 2023 Jan 6;51(D1):D1129-D1137. doi: 10.1093/nar/gkac732.
R-loops are three-stranded nucleic acid structures formed from the hybridization of RNA and DNA. In 2012, Ginno et al. introduced the first R-loop mapping method. Since that time, dozens of R-loop mapping studies have been conducted, yielding hundreds of publicly available datasets. Current R-loop databases provide only limited access to these data. Moreover, no web tools for analyzing user-supplied R-loop datasets have yet been described. In our recent work, we reprocessed 810 R-loop mapping samples, building the largest R-loop data resource to date. We also defined R-loop consensus regions and developed a framework for R-loop data analysis. Now, we introduce RLBase, a user-friendly database that provides the capability to (i) explore hundreds of public R-loop mapping datasets, (ii) explore R-loop consensus regions, (iii) analyze user-supplied data and (iv) download standardized and reprocessed datasets. RLBase is directly accessible via the following URL: https://gccri.bishop-lab.uthscsa.edu/shiny/rlbase/.
R 环是由 RNA 和 DNA 杂交形成的三链核酸结构。2012 年，Ginno 等人引入了第一个 R 环作图方法。从那时起，已经进行了数十项 R 环作图研究，产生了数百个公开可用的数据集。目前的 R 环数据库仅提供对这些数据的有限访问。此外，还没有用于分析用户提供的 R 环数据集的网络工具。在我们最近的工作中，我们重新处理了 810 个 R 环作图样本，构建了迄今为止最大的 R 环数据资源。我们还定义了 R 环一致区域，并开发了 R 环数据分析框架。现在，我们引入了 RLBase，这是一个用户友好的数据库，具有以下功能：（i）探索数百个公开的 R 环作图数据集，（ii）探索 R 环一致区域，（iii）分析用户提供的数据，（iv）下载标准化和重新处理的数据集。RLBase 可通过以下网址直接访问：https://gccri.bishop-lab.uthscsa.edu/shiny/rlbase/。
