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. 2019 Jan 8;47(D1):D63-D68.
doi: 10.1093/nar/gky904.

CRISPRlnc: A Manually Curated Database of Validated sgRNAs for lncRNAs

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Free PMC article

CRISPRlnc: A Manually Curated Database of Validated sgRNAs for lncRNAs

Wen Chen et al. Nucleic Acids Res. .
Free PMC article

Abstract

The CRISPR/Cas9 system, as a revolutionary genome editing tool for all areas of molecular biology, provides new opportunities for research on lncRNA's function. However, designing a CRISPR/Cas9 single guide RNA (sgRNA) for lncRNA is not easy with an unwarrantable effectiveness. Thus, it is worthy of collecting validated sgRNAs, to assist in efficiently choosing sgRNA with an expected activity. CRISPRlnc (http://www.crisprlnc.org or http://crisprlnc.xtbg.ac.cn) is a manually curated database of validated CRISPR/Cas9 sgRNAs for lncRNAs from all species. After manually reviewing more than 200 published literature, the current version of CRISPRlnc contains 305 lncRNAs and 2102 validated sgRNAs across eight species, including mammalian, insect and plant. We handled the ID, position in the genome, sequence and functional description of these lncRNAs, as well as the sequence, protoacceptor-motif (PAM), CRISPR type and validity of their paired sgRNAs. In CRISPRlnc, we provided the tools for browsing, searching and downloading data, as well as online BLAST service and genome browse server. As the first database against the validated sgRNAs of lncRNAs, CRISPRlnc will provide a new and powerful platform to promote CRISPR/Cas9 applications for future functional studies of lncRNAs.

Figures

Figure 1.
Figure 1.
Overview of the CRISPRlnc database.
Figure 2.
Figure 2.
Statistics of the CRISPRlnc database. (A) The distribution of sgRNAs in various species. (B) The functional types of sgRNA. (C) The Top10 lncRNAs that possess known designed sgRNAs, without regard to those high-throughput experimental data. (D) The position distribution of sgRNAs on lncRNAs.
Figure 3.
Figure 3.
User interface of the CRISPRlnc database. (A) The ‘Browse’ page. (B) ‘GBrowse’, the genome browser. (C) The ‘Details’ page. (D) ‘Online BLAST’ search. (E) The ‘Advanced Search’ page.

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