CRISPRz: A database of zebrafish validated sgRNAs

Nucleic Acids Research

Volumn 44, Issue D1, 2016, Pages D822-D826

  Varshney, Gaurav K ^a   Zhang, Suiyuan ^a   Pei, Wuhong ^a   Adomako Ankomah, Ashrifia ^a   Fohtung, Jacob ^a   Schaffer, Katherine ^a   Carrington, Blake ^a   Maskeri, Anoo ^a   Slevin, Claire ^a   Wolfsberg, Tyra ^a   Ledin, Johan ^b   Sood, Raman ^a   Burgess, Shawn M ^a  

^a NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

RNA; SINGLE GUIDE RNA; UNCLASSIFIED DRUG;

ARTICLE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CRISPR CAS SYSTEM; CRISPRZ DATABASE; DATA BASE; GENE MUTATION; GENETIC BACKGROUND; MUTAGENICITY; MUTANT; NONHUMAN; PRIORITY JOURNAL; ZEBRA FISH; ANIMAL; EMBRYOLOGY; GENE TARGETING; GENETIC DATABASE; GENETICS; HUMAN; MOUSE; MUTAGENESIS;

ANIMALS; CRISPR-CAS SYSTEMS; DATABASES, GENETIC; GENE TARGETING; HUMANS; MICE; MUTAGENESIS; RNA; ZEBRAFISH;

EID: 84976864113     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv998     Document Type: Article

References (30)

1. Garneau, J. E., Dupuis, M. E., Villion, M., Romero, D. A., Barrangou, R., Boyaval, P., Fremaux, C., Horvath, P., Magadan, A. H. and Moineau, S. (2010) The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature, 468, 67-71.
2. Gasiunas, G., Barrangou, R., Horvath, P. and Siksnys, V. (2012) Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc. Natl. Acad. Sci. U. S. A., 109, E2579-E2586.
3. Sapranauskas, R., Gasiunas, G., Fremaux, C., Barrangou, R., Horvath, P. and Siksnys, V. (2011) The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic Acids Res., 39, 9275-9282.
4. Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A. and Charpentier, E. (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 337, 816-821.
5. Chang, N., Sun, C., Gao, L., Zhu, D., Xu, X., Zhu, X., Xiong, J. W. and Xi, J. J. (2013) Genome editing with RNA-guided Cas9 nuclease in zebrafish embryos. Cell Res., 23, 465-472.
6. Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A. et al. (2013) Multiplex genome engineering using CRISPR/Cas systems. Science, 339, 819-823.
7. Hwang, W. Y., Fu, Y., Reyon, D., Maeder, M. L., Tsai, S. Q., Sander, J. D., Peterson, R. T., Yeh, J. R. and Joung, J. K. (2013) Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat. Biotechnol., 31, 227-229.
8. Jao, L. E., Wente, S. R. and Chen, W. (2013) Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system. Proc. Natl. Acad. Sci. U. S. A., 110, 13904-13909.
9. Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., Norville, J. E. and Church, G. M. (2013) RNA-guided human genome engineering via Cas9. Science, 339, 823-826.
10. Sternberg, S. H. and Doudna, J. A. (2015) Expanding the Biologist's Toolkit with CRISPR-Cas9. Mol. Cell, 58, 568-574.
11. Hsu, P. D., Lander, E. S. and Zhang, F. (2014) Development and applications of CRISPR-Cas9 for genome engineering. Cell, 157, 1262-1278.
12. Varshney, G. K., Pei, W., LaFave, M. C., Idol, J., Xu, L., Gallardo, V., Carrington, B., Bishop, K., Jones, M., Li, M. et al. (2015) High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9. Genome Res., 25, 1030-1042.
13. Auer, T. O., Duroure, K., De Cian, A., Concordet, J. P. and Del Bene, F. (2014) Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair. Genome Res., 24, 142-153.
14. Hisano, Y., Sakuma, T., Nakade, S., Ohga, R., Ota, S., Okamoto, H., Yamamoto, T. and Kawahara, A. (2015) Precise in-frame integration of exogenous DNA mediated by CRISPR/Cas9 system in zebrafish. Sci. Rep., 5, 8841.
15. Kimura, Y., Hisano, Y., Kawahara, A. and Higashijima, S. (2014) Efficient generation of knock-in transgenic zebrafish carrying reporter/driver genes by CRISPR/Cas9-mediated genome engineering. Sci. Rep., 4, 6545.
16. Shah, A. N., Davey, C. F., Whitebirch, A. C., Miller, A. C. and Moens, C. B. (2015) Rapid reverse genetic screening using CRISPR in zebrafish. Nat. Methods, 12, 535-540.
17. Moreno-Mateos, M. A., Vejnar, C. E., Beaudoin, J.-D., Fernandez, J. P., Mis, E. K., Khokha, M. K. and Giraldez, A. J. (2015) CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat. Methods, 12, 982-988.
18. Gagnon, J. A., Valen, E., Thyme, S. B., Huang, P., Ahkmetova, L., Pauli, A., Montague, T. G., Zimmerman, S., Richter, C. and Schier, A. F. (2014) Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. PLoS One, 9, e98186.
19. Ablain, J., Durand, E. M., Yang, S., Zhou, Y. and Zon, L. I. (2015) A CRISPR/Cas9 vector system for tissue-specific gene disruption in zebrafish. Dev. Cell, 32, 756-764.
20. Hruscha, A., Krawitz, P., Rechenberg, A., Heinrich, V., Hecht, J., Haass, C. and Schmid, B. (2013) Efficient CRISPR/Cas9 genome editing with low off-target effects in zebrafish. Development, 140, 4982-4987.
21. Irion, U., Krauss, J. and Nusslein-Volhard, C. (2014) Precise and efficient genome editing in zebrafish using the CRISPR/Cas9 system. Development, 141, 4827-4830.
22. Kleinstiver, B. P., Prew, M. S., Tsai, S. Q., Topkar, V. V., Nguyen, N. T., Zheng, Z., Gonzales, A. P., Li, Z., Peterson, R. T., Yeh, J. R. et al. (2015) Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature, 523, 481-485.
23. Li, J., Zhang, B. B., Ren, Y. G., Gu, S. Y., Xiang, Y. H. and Du, J. L. (2015) Intron targeting-mediated and endogenous gene integrity-maintaining knockin in zebrafish using the CRISPR/Cas9 system. Cell Res., 25, 634-637.
24. Liu, D., Wang, Z., Xiao, A., Zhang, Y., Li, W., Zu, Y., Yao, S., Lin, S. and Zhang, B. (2014) Efficient gene targeting in zebrafish mediated by a zebrafish-codon-optimized cas9 and evaluation of off-targeting effect. J. Genet. Genomics, 41, 43-46.
25. Ota, S., Hisano, Y., Ikawa, Y. and Kawahara, A. (2014) Multiple genome modifications by the CRISPR/Cas9 system in zebrafish. Genes Cells, 19, 555-564.
26. Qin, W., Liang, F., Feng, Y., Bai, H., Yan, R., Li, S. and Lin, S. (2015) Expansion of CRISPR/Cas9 genome targeting sites in zebrafish by Csy4-based RNA processing. Cell Res., 25, 1074-1077.
27. Santoriello, C. and Zon, L. I. (2012) Hooked! Modeling human disease in zebrafish. J. Clin. Invest., 122, 2337-2343.
28. Hruscha, A. and Schmid, B. (2015) Generation of zebrafish models by CRISPR/Cas9 genome editing. Methods Mol. Biol., 1254, 341-350.
29. Sood, R., Carrington, B., Bishop, K., Jones, M., Rissone, A., Candotti, F., Chandrasekharappa, S. C. and Liu, P. (2013) Efficient methods for targeted mutagenesis in zebrafish using zinc-finger nucleases: data from targeting of nine genes using CompoZr or CoDA ZFNs. PLoS One, 8, e57239.
30. Carrington, B., Varshney, G. K., Burgess, S. M. and Sood, R. (2015) CRISPR-STAT: an easy and reliable PCR-based method to evaluate target-specific sgRNA activity. Nucleic Acids Res., doi:10.1093/nar/gkv802.