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PI: Dr. James C.-K. Shen ( 沈哲鯤 ) Co-PI: Dr. Michael Hsiao ( 蕭宏昇副研究員 )

10/16/98. C6-The RNAi Core. PI: Dr. James C.-K. Shen ( 沈哲鯤 ) Co-PI: Dr. Michael Hsiao ( 蕭宏昇副研究員 ) Co-PI/ Manager : Dr. King-Song Jeng ( 鄭金松副技師 ) Speaker: King-Song Jeng ( 鄭金松 ) Institute of Molecular Biology / Genomic Research Center Academia Sinica

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PI: Dr. James C.-K. Shen ( 沈哲鯤 ) Co-PI: Dr. Michael Hsiao ( 蕭宏昇副研究員 )

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  1. 10/16/98 C6-The RNAi Core PI: Dr. James C.-K. Shen (沈哲鯤) Co-PI: Dr. Michael Hsiao (蕭宏昇副研究員) Co-PI/ Manager: Dr. King-Song Jeng (鄭金松副技師) Speaker: King-Song Jeng (鄭金松) Institute of Molecular Biology / Genomic Research Center Academia Sinica Sponsored by National Research Program for Genomic Medicine, National Science Council/ Academia Sinica 1

  2. Outline • The RNAi Consortium (TRC) • Current status of the RNAi Core • Collaboration Research Project 2

  3. The RNAi Consortium (TRC) Objectives: • Create genome wide, renewable RNAi reagents for research and educational uses; • Develop, validate and optimize materials, methodologies and information for their effective application in research. 3

  4. Phases of TRC Program The RNAi Consortium (TRC)The RNAi Core Phase I (May/2004 to Apr/2007) Jun/2005 to Apr/2008 Phase II (Oct/2007 to Sept/2011) May/2008 to Apr/2011 4

  5. Composition of TRC-I and TRC-II * HMS: Harvard Medical School 5

  6. Lentivirus-based RNAi (VSV-G peudotyped virus) shRNA 6 http://www.accessexcellence.org/RC/VL/GG/retrovirus.html

  7. Vector Used by TRC/RNAi Core AgeI (ACCGGT) EcoRI (GAATTC) 7 http://www.sigmaaldrich.com/Area_of_Interest/Life_Science/Functional_Genomics_and_RNAi/Product_Lines/shRNA_Library.html

  8. TRC2 library goals More powerful library: – enriched for best OT KD shRNAs – even coverage of genome High-performing existing clones TRC2 library 3+ good shRNAs per gene (test) New clones

  9. Materials Received from TRC • shRNA constructs and knockdown information: • Pooled genome-wide shRNA plasmid DNAs and chips (human and mouse) for RNAi genome-wide screening. 9

  10. TRC shRNA performance stats: Sept.09 67,000 TRC shRNAs targeting 12,200 genes (Jurkat data excluded) All Hairpins Statistics Per Gene Statistics J. Grenier 10

  11. How reproducible are the data?: How consistent is the > 70% call? Trial 1 Consistent ‘pass call’ 75% of the time. 33% of inconsistent calls are > 60% KD in the failed rep 50% of inconsistent calls are < 80% KD in the passed rep Trial 2 Total hairpins: 3495 Jen Grenier, Shuba Gopal

  12. RNAi CORE TAIWAN TRC 12

  13. National RNAi Core (Since June 2005) • Housed in Genomics Research Center (GRC) and Institute of Molecular Biology (IMB) • Connected to TRC-I and TRC-II • Responsible for • Services • Technology R&D • Collaborative research activities • Welcome local and international collaborations 13

  14. Aims of RNAi Core: Third Phase Objectives: • Maximizing the utilization of the RNAi library in mammalian genetic screen 14

  15. Routine Service Items 15

  16. Analyses of Geographic Distribution and Distributed Items to the Users Total Users: 465 PIs Total Users: 465 PIs 3% 2% 20% 11% 6% 13% 8% 58% 79% Academia Sinica(AS • ): 11% Bacterium: 79% N. Taiwan(AS not included): 58% Virus: 6% Middle Taiwan: 8% Lentiviral vector: 13% Southern Taiwan: 20% Eastern Taiwan: 3% HTC image analysis: 2% 16

  17. User Publication 20 25 20 18 16 18 16 16 14 12 14 12 12 10 # of publication # of publication 10 8 8 6 5 6 6 4 4 4 2 2 0 <5 5~10 >10 0 2009~2010 2006~2007 2008~2009 Impact Factor Year Please acknowledge the RNAi Core for RNAi reagents when your research is get published. Please refer to http://rnai.genmed.sinica.edu.tw/faq-detail.asp?sn=16 for example. 17

  18. Items Plan to Be Served in the Future • Genome-wide RNAi pooled screening • Produce/ provide shRNA-expressing lentivirus defined by User (a 2D barcode shRNA plasmid DNAs library is being established) • Enlarge the activity of RNAi library screening • C5: perform microarray and data analysis • C6: provide pooled virus 18

  19. Collaborative Research Project(s) workflow and regulations Discuss on the Potential project • Current regulations: • Tying with the workload of the Core ; • Sharing cost and labor; Submission Re-submission • Future capacity • Could accommodate more projects if transform Core into National RNAi Screening Center (NRSC). No Review by committee Reject or Revise Yes Yes Notify user committee RNAi screen and data analysis Data arrangement and release Case closed 19

  20. Contact Information 中央研究院基因體研究中心四樓RNAi Core Lab. 核心電話: 02-27899724 (分機 15) 鍾穎麗小姐核心傳真: 02-27885420服務信箱: RNAiCore@imb.sinica.edu.tw核心網址: http://rnai.genmed.sinica.edu.tw/index.asp 核心地址: 台北市南港區115研究院路二段128號 20

  21. Thank you 21

  22. Navigation of RNAiWebsite Chi-long Lin

  23. Navigation of RNAi website • Overview • Search function • Knockdown information database • New Online Ordering system • Feedback mechanism

  24. Navigation of RNAi website • Overview • Search function • Knockdown information database • New Online Ordering system • Feedback mechanism

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