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Exploration and analysis of R-loop mapping data with RLBase
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 d...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825527/ https://www.ncbi.nlm.nih.gov/pubmed/36039757 http://dx.doi.org/10.1093/nar/gkac732 |
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author | Miller, Henry E Montemayor, Daniel Li, Janet Levy, Simon A Pawar, Roshan Hartono, Stella Sharma, Kumar Frost, Bess Chedin, Frédéric Bishop, Alexander J R |
author_facet | Miller, Henry E Montemayor, Daniel Li, Janet Levy, Simon A Pawar, Roshan Hartono, Stella Sharma, Kumar Frost, Bess Chedin, Frédéric Bishop, Alexander J R |
author_sort | Miller, Henry E |
collection | PubMed |
description | 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/. |
format | Online Article Text |
id | pubmed-9825527 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-98255272023-01-10 Exploration and analysis of R-loop mapping data with RLBase Miller, Henry E Montemayor, Daniel Li, Janet Levy, Simon A Pawar, Roshan Hartono, Stella Sharma, Kumar Frost, Bess Chedin, Frédéric Bishop, Alexander J R Nucleic Acids Res Database Issue 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/. Oxford University Press 2022-08-30 /pmc/articles/PMC9825527/ /pubmed/36039757 http://dx.doi.org/10.1093/nar/gkac732 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Database Issue Miller, Henry E Montemayor, Daniel Li, Janet Levy, Simon A Pawar, Roshan Hartono, Stella Sharma, Kumar Frost, Bess Chedin, Frédéric Bishop, Alexander J R Exploration and analysis of R-loop mapping data with RLBase |
title | Exploration and analysis of R-loop mapping data with RLBase |
title_full | Exploration and analysis of R-loop mapping data with RLBase |
title_fullStr | Exploration and analysis of R-loop mapping data with RLBase |
title_full_unstemmed | Exploration and analysis of R-loop mapping data with RLBase |
title_short | Exploration and analysis of R-loop mapping data with RLBase |
title_sort | exploration and analysis of r-loop mapping data with rlbase |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825527/ https://www.ncbi.nlm.nih.gov/pubmed/36039757 http://dx.doi.org/10.1093/nar/gkac732 |
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