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Ling V. Sun & Li Wang

PBmice and MP-PBmice: A database system of PiggyBac (PB) insertional mutations in mice and a subsystem for mapping the mutations onto the mouse genome with large-scale experimental data. Ling V. Sun & Li Wang.

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Ling V. Sun & Li Wang

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  1. PBmice and MP-PBmice: A database system of PiggyBac (PB) insertional mutations in mice and a subsystem for mapping the mutations onto the mouse genome with large-scale experimental data Ling V. Sun & Li Wang Institute of Developmental Biology and Molecular Medicine , Fudan University, and Shanghai Center for Bioinformation Technology, China

  2. Transposons and Insertional Mutations Transposons: Mobile Genetic Elements Transposon Transposon Transposon 基 因 Transposon Transgenesis Barbara McClintock Insertional Mutagenesis chromosome Gene Mutant Gene Tagged

  3. Advantages of Insertional Mutations • can produce easily tractable mutations • can produce large number of mutants at low cost and high speed

  4. PBase PB end PB[RFP] Act-PBase + PB(PiggyBac): a high efficient transposition system in mammals Moth piggyBac (Cary et al. Virology 1989) Mammal PB system (Ding et al. Cell 2005)

  5. PB: an ideal tool for insertional mutagenesis Traditional Knock-out PB insertional mutagenesis Molecular cloning ES Reduce Cost & Improve Efficiency Screen cell lines Micro-injection IVF Breeding PB Mutant Mutant 1 Mutant 2 Mutant 3

  6. http://www.idmshanghai.cn/PBmice

  7. INSERT interface

  8. MP-PBmice system (insertional mutations mapping system of PBmice • Experimental Procedure • Flow production

  9. From PBmice to MP-PBmice • Integrated information of PB insertional mutations and their characterizations in mice: PBmice (NAR, 2008 vol.36, Http://www.idmshanghai.cn/PBmice) • Daily book-keeping and information exchange between experimental groups for the mapping procedure: MP-PBmice

  10. Design and implementation • User Interfaces • Features

  11. MP-PBmice • Design and implementation • User Interface • Features

  12. Database Tables: the relational data schema • Access-control Table • Experimental Stage Table • Constant Table • Status Table

  13. Model-View-Controller (MVC) Pattern & Struts-Spring-Hibernate (SSH) Framework

  14. MP-PBmice • Design and implementation • User Interfaces • Features

  15. viewDetail detailed information page comment box

  16. MP-PBmice • Design and implementation • User Interface • Features

  17. Strict Access Control

  18. Work Flow Control

  19. Expandability • Suitable for any genome • Suitable for any experimental mapping method

  20. Future Plan • Improve PBmice Mapping Database • Add Bioinformatics Tools Needed

  21. Acknowledgments Wenwei Yang Min Han Yuan Zhuang Tian Xu Xiaohui Wu Yun Zheng Ke Jin Jigang Yang Yang Zhong Xing Xie Dongsheng Li Ning Gu For collaboration and further contact: Dr. Ling V. Sun (PI): Lingsun@fudan.edu.cn

  22. Thanks

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