Exploration and analysis of R-loop mapping data with RLBase
Abstract
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/.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Aug 30, 2022
- Source ID
- 10.1093/nar/gkac732
Entities
People
- Alexander J R Bishop
- Bess Frost
- Daniel Montemayor
- Frédéric Chedin
- Henry E Miller
- Janet Li
- Kumar Sharma
- Roshan Pawar
- Simon A Levy
- Stella Hartono
Organizations
- Cancer Prevention and Research Institute of Texas
- National Institutes of Health
- United States Department of Defense
- University of British Columbia
- University of California, Davis
- University of Texas Health Science Center at San Antonio