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BioMed Research International
Volume 2013, Article ID 270805, 4 pages
http://dx.doi.org/10.1155/2013/270805
Research Article

A Guide RNA Sequence Design Platform for the CRISPR/Cas9 System for Model Organism Genomes

1Biomedical Engineering Department, College of Engineering, Peking University, Beijing 100871, China
2Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
3National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
4Institute of Computer Science and Technology, Peking University, Beijing 100871, China

Received 4 July 2013; Accepted 13 September 2013

Academic Editor: Yi Zhao

Copyright © 2013 Ming Ma et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. J. C. Miller, M. C. Holmes, J. Wang et al., “An improved zinc-finger nuclease architecture for highly specific genome editing,” Nature Biotechnology, vol. 25, no. 7, pp. 778–785, 2007. View at Publisher · View at Google Scholar · View at Scopus
  2. J. D. Sander, E. J. Dahlborg, M. J. Goodwin et al., “Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA),” Nature Methods, vol. 8, no. 1, pp. 67–69, 2011. View at Publisher · View at Google Scholar · View at Scopus
  3. M. Christian, T. Cermak, E. L. Doyle et al., “Targeting DNA double-strand breaks with TAL effector nucleases,” Genetics, vol. 186, no. 2, pp. 756–761, 2010. View at Publisher · View at Google Scholar · View at Scopus
  4. J. C. Miller, S. Tan, G. Qiao et al., “A TALE nuclease architecture for efficient genome editing,” Nature Biotechnology, vol. 29, no. 2, pp. 143–148, 2011. View at Publisher · View at Google Scholar · View at Scopus
  5. D. Reyon, S. Q. Tsai, C. Khayter, J. A. Foden, J. D. Sander, and J. K. Joung, “FLASH assembly of TALENs for high-throughput genome editing,” Nature Biotechnology, vol. 30, no. 5, pp. 460–465, 2012. View at Google Scholar
  6. L. Tesson, C. Usal, S. Menoret et al., “Knockout rats generated by embryo microinjection of TALENs,” Nature Biotechnology, vol. 29, no. 8, pp. 695–696, 2011. View at Publisher · View at Google Scholar · View at Scopus
  7. C. Tong, G. Huang, C. Ashton, H. Wu, H. Yan, and Q. L. Ying, “Rapid and cost-effective gene targeting in rat embryonic stem cells by TALENs,” Journal of Genetics and Genomics, vol. 39, no. 6, pp. 275–280, 2012. View at Google Scholar
  8. J. D. Sander, L. Cade, C. Khayter et al., “Targeted gene disruption in somatic zebrafish cells using engineered TALENs,” Nature Biotechnology, vol. 29, no. 8, pp. 697–698, 2011. View at Publisher · View at Google Scholar · View at Scopus
  9. P. Mali, L. Yang, K. M. Esvelt et al., “RNA-guided human genome engineering via Cas9,” Science, vol. 339, no. 6121, pp. 823–826, 2013. View at Google Scholar
  10. L. Cong, F. A. Ran, D. Cox et al., “Multiplex genome engineering using CRISPR/Cas systems,” Science, vol. 339, no. 6121, pp. 819–823, 2013. View at Google Scholar
  11. M. Villion and S. Moineau, “The double-edged sword of CRISPR-Cas systems,” Cell Research, vol. 23, no. 1, pp. 15–17, 2013. View at Google Scholar
  12. H. Wang, H. Yang, C. S. Shivalila et al., “One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering,” Cell, vol. 153, no. 4, pp. 910–918, 2013. View at Google Scholar
  13. N. Chang, C. Sun, L. Gao et al., “Genome editing with RNA-guided Cas9 nuclease in zebrafish embryos,” Cell Research, vol. 23, no. 4, pp. 465–472, 2013. View at Google Scholar
  14. K. S. Makarova, D. H. Haft, R. Barrangou et al., “Evolution and classification of the CRISPR-Cas systems,” Nature Reviews Microbiology, vol. 9, no. 6, pp. 467–477, 2011. View at Publisher · View at Google Scholar · View at Scopus
  15. B. Langmead, C. Trapnell, M. Pop, and S. L. Salzberg, “Ultrafast and memory-efficient alignment of short DNA sequences to the human genome,” Genome Biology, vol. 10, no. 3, article R25, 2009. View at Publisher · View at Google Scholar · View at Scopus
  16. H. Li, “Tabix: fast retrieval of sequence features from generic TAB-delimited files,” Bioinformatics, vol. 27, no. 5, pp. 718–719, 2011. View at Publisher · View at Google Scholar · View at Scopus
  17. S. T. Sherry, M.-H. Ward, M. Kholodov et al., “DbSNP: the NCBI database of genetic variation,” Nucleic Acids Research, vol. 29, no. 1, pp. 308–311, 2001. View at Google Scholar · View at Scopus
  18. A. McKenna, M. Hanna, E. Banks et al., “The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data,” Genome Research, vol. 20, no. 9, pp. 1297–1303, 2010. View at Publisher · View at Google Scholar · View at Scopus
  19. R. Lorenz, S. H. Bernhart, C. Höner Zu Siederdissen et al., “ViennaRNA package 2.0,” Algorithms for Molecular Biology, vol. 6, no. 1, article 26, 2011. View at Publisher · View at Google Scholar · View at Scopus
  20. W. Jiang, D. Bikard, D. Cox, F. Zhang, and L. A. Marraffini, “RNA-guided editing of bacterial genomes using CRISPR-Cas systems,” Nature Biotechnology, vol. 31, no. 3, pp. 233–239, 2013. View at Google Scholar
  21. Y. Fu, J. A. Foden, C. Khayter et al., “High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cell,” Nature Biotechnology, vol. 31, pp. 822–826, 2013. View at Google Scholar