crisprSQL: a novel database platform for CRISPR/Cas off-target cleavage assays
Open accessAbstract
With ongoing development of the CRISPR/Cas programmable nuclease system, applications in the area of in vivo therapeutic gene editing are increasingly within reach. However, non-negligible off-target effects remain a major concern for clinical applications. Even though a multitude of off-target cleavage datasets have been published, a comprehensive, transparent overview tool has not yet been established. Here, we present crisprSQL (http://www.crisprsql.com), an interactive and bioinformatically enhanced collection of CRISPR/Cas9 off-target cleavage studies aimed at enriching the fields of cleavage profiling, gene editing safety analysis and transcriptomics. The current version of crisprSQL contains cleavage data from 144 guide RNAs on 25,632 guide-target pairs from human and rodent cell lines, with interaction-specific references to epigenetic markers and gene names. The first curated database of this standard, it promises to enhance safety quantification research, inform experiment design and fuel development of computational off-target prediction algorithms.
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Multiplex genome-editing technologies for revolutionizing plant biology and crop improvement
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- Authors
- Störtz, F., & Minary, P.
- Affiliations
- University of Oxford (GB)
- Department of Computer Science, University of Oxford, Parks Road, Oxford OX1 3QD, UK
- Corresponding author
- Störtz, Florian
- ORCID
- Störtz, Florian
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-10-21
- Volume
- 49
- Issue
- D1
- Pages
- D855-D861
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC7778913
- OpenAlex
- W3093632917
- Cited by
- 37
- References
- 48
- Citations by year
- 2026: 3 · 2025: 12 · 2024: 8 · 2023: 3 · 2022: 7 · 2021: 4
- FWCI
- 1.14
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Biotechnology and Biological Sciences Research Council (BB/M011224/1, BB/S507593/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Interference and Gene Delivery
- Keywords
- CRISPR/Cas9, off-target cleavage, database platform, guide RNA, gene editing safety, transcriptomics, epigenetic modifications, off-target prediction, therapeutic gene editing
- MeSH terms
- Biological Assay, Streptococcus pyogenes, User-Computer Interface, Databases, Genetic, Epigenesis, Genetic, DNA Cleavage, CRISPR-Cas Systems
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