SYNTHETIC BIOLOGY DNA ASSEMBLY SINGLE-CELL GENOMICS DRUG DISCOVERY. The Royal Society of Edinburgh Conference Centre. Hosted by

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1 SYNTHETIC BIOLOGY DNA ASSEMBLY SINGLE-CELL GENOMICS DRUG DISCOVERY The Royal Society of Edinburgh Conference Centre Wolfsen Lecture Theatre Hosted by

2 LABCYTE EDINBURGH 2016 The Royal Society of Edinburgh Conference Centre, Edinburgh SEPTEMBER, 2016 WEDNESDAY, 28 September Synthetic Biology Drug Discovery Single-cell Genomics Track / Time Title of Presentation Presenter 12:00 1:00 PM LUNCH SERVED Upper and lower galleries Session Chair Dr. Patrick Cai, University of Edinburgh 1:00 1:15 PM Welcome Address Mark Fischer-Colbrie CEO, Labcyte Inc. 1:15 1:55 PM Making Synthetic Genomes with the Echo Acoustic Liquid Handler Dr. Patrick Cai Autodesk Distinguished Scholar, Co-Director, Edinburgh Genome Foundry; Chancellor s Fellow, University of Edinburgh 1:55 2:35 PM Using Systems Approaches to Understand the Emergence of Phenotypic Heterogeneity Dr. Chris Bakal Team Leader, The Institute of Cancer Research 2:35 3:15 PM Single-cell Genomics at the DOE, Joint Genome Institute Dr. Robert Bowers Research Scientist, Dept. of Energy, Joint Genome Institute 3:15 3:35 PM BREAK Session Chair Dr. Sunil Chandran, Amyris Inc. 3:35 4:15 PM Building Scalable Workflows for DNA Assembly Using BASIC Building Blocks Dr. David McClymont Head of Automation, SynbiCITE, Imperial College London 4:15 4:55 PM High-throughput Screenings in Neurodegenerative Diseases Marc Emmenegger Ph.D. Student, Institute of Neuropathology, University Hospital Zurich 4:55 5:05 PM BREAK 5:05 5:35 PM Challenges and Opportunities for Miniaturization of Workflows in Synthetic Biology Dr. Linda D Amore Operational Manager, GeneMill Foundry University of Liverpool 5:35 6:10 PM Implementation of Acoustic Dispensing into HT Single Cell Sequencing Workflows Dr. Stephan Lorenz Head of Single Cell Genomics Core Facility, Wellcome Trust Sanger institute 7:30 10:00 PM The Scotch Whisky Experience and Dinner The Scotch Whisky Experience 354 Castlehill The Royal Mile, Edinburgh Tel: PROGRAM GUIDE: Labcyte - Edinburgh 2016

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4 THURSDAY, 29 September Synthetic Biology Drug Discovery Single-cell Genomics Track / Time Title of Presentation Presenter 9:00 9:30 AM COFFEE Upper gallery 9:30 9:40 AM Welcome to 2nd Day Labcyte 9:40 10:20 AM Miniaturisation, Automation and Development of Novel Genomic Applications with Echo 525 and Access System Dr. David Simpson Senior Lecturer, Queen s University Belfast 10:20 11:00 AM Automation Needs for a High Throughput Genomics Facility Dr. Paolo Piazza Section Leader, High Throughput Sequencing Library Prep and Genomics Process Improvement, Wellcome Trust Centre for Human Genetics 11:00 11:40 AM RNAi Screening and Cell Based Assay Program at FIMM: The Impact of Acoustic Dispensing to Improve Process Flows Dr. Jani Saarela Operational Manager, FIMM - Institute for Molecular Medicine Finland 11:40 12:50 PM LUNCH Upper and lower galleries Session Chair Dr. Stephan Lorenz, Sanger Institute 12:50 1:30 PM Recruitment of a Robotic Workforce for Large-scale Construct Assembly Dr. Andy Breakspear Research Assistant, John Innes Centre 1:30 2:10 PM High Throughput Platform for Strain Optimization and Screening: Reducing the Cost and Time for Commercializing Novel Molecules Dr. Sunil Chandran Senior Director, Amyris Inc. 2:10 2:50 PM A Generic, Cost-effective and Scalable Cell Lineage Analysis Platform Dr. Tamir Biezuner Research Scientist, Weizmann Institute of Science 2:50 3:00 PM Closing Remarks Labcyte 4 PROGRAM GUIDE: Labcyte - Edinburgh 2016

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6 LABCYTE EDINBURGH 2016 The Royal Society of Edinburgh Conference Centre, Edinburgh SEPTEMBER, 2016 Synthetic Biology Drug Discovery Single-cell Genomics Dr. Patrick Cai Autodesk Distinguished Scholar, Co-Director, Edinburgh Genome Foundry; Chancellor s Fellow, University of Edinburgh 1:15 PM Making Synthetic Genomes with the Echo Acoustic Liquid Handling Dr. Patrick Yizhi Cai received his bachelor s degree in Computer Science in China, a master s degree in Bioinformatics from University of Edinburgh in the UK, and a Ph.D. in Genetics, Bioinformatics, and Computational Biology from Virginia Tech in the U.S. Dr. Cai has his postdoctoral fellowship under Jef Boeke at the Johns Hopkins University School of Medicine. He serves as a senior scientific consultant to Beijing Genomics Institute, and is the first Autodesk Distinguished Scholar. Starting summer 2013, Dr. Cai started his own research group at the University of Edinburgh with a prestigious Chancellor s Fellowship, and his lab focuses on Computer Assisted Design for Synthetic Biology, NeoChromosome design and synthesis in the yeast, and DNA assembly automation. Dr. Cai founded and directs Edinburgh Genome Foundry, a UK national facility for automated DNA synthesis and assembly. Dr. Chris Bakal Team Leader, The Institute of Cancer Research 1:55 PM Using Systems Approaches to Understand the Emergence of Phenotypic Heterogeneity Dr. Chris Bakal received his BSc in Biochemistry from the University of British Columbia, and his PhD in Medical Biophysics at the University of Toronto. Dr. Bakal s postdoctoral work was performed in the laboratory of Norbert Perrimon at Harvard Medical School, during which time he was also an affiliate of the Computer Science and Artificial Intelligence Laboratory (CSAIL) at MIT. After being awarded a Wellcome Trust Career Development Fellowship, Dr. Bakal established his laboratory at the Institute of Cancer Research in London in The Bakal laboratory s research is aimed at understanding how signaling networks regulate cell fate decisions in cancer cells by leveraging expertise in single cell biology, communication systems, and computational technologies. In particular, the Bakal lab has pioneered the use of automated image analysis and machine-learning to describe the signaling dynamics regulating cell morphogenesis and proliferation. Dr. Bakal was recently awarded the 2015 Cancer Research UK Future Leaders Prize. In 2014, he was awarded the Council for Systems Biology Merrimack Pharmaceuticals Prize, and in 2013 the British Association for Cancer Research Frank Rose Award. Outside of science Dr. Bakal is competitive road cyclist, and a former world-ranked downhill ski racer. Dr. Robert Bowers Research Scientist, U.S. Department of Energy (DOE), Joint Genome Institute 2:35 PM Single-cell Genomics at the DOE, Joint Genome Institute Dr. Robert Bowers is currently a research scientist at the DOE Joint Genome Institute. He is involved in a number of projects ranging from internal production and R&D to projects addressing novel scientific questions. As a member of the Microbial Genomics Program, he contributes to both the single-cell production and analysis pipelines, as well as leading specific research projects. Within the single-cell program, he and his team take advantage of a variety of cultivation independent approaches in order to better understand microbial systems. For example, Dr. Bowers and his team frequently use a combination of bulk sample metagenomics together with single-cell genomics to better understand the underlying principles that govern microbial interactions within an environmental context. In Dr. Bower s presentation at the Symposium, he will briefly describe the JGI infrastructure and programs, the organization s current single-cell production pipeline, and provide an overview of a project where they re extending the application of single-cell genomics to illuminate previously unknown branches on the microbial tree of life. 6 PROGRAM GUIDE: Labcyte - Edinburgh 2016

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8 Synthetic Biology Drug Discovery Single-cell Genomics Dr. David McClymont Head of Automation, SynbiCITE, Imperial College London 3:35 PM Building Scalable Workflows for DNA Assembly using BASIC Building Blocks Dr. David McClymont completed his PhD in Molecular Pharmacology at the University of Nottingham and afterward moved to Xention Discovery to carry out assay development using automated patch clamp systems for ion channel drug discovery. This led to a keen interest in automation and subsequently to a role at the Chemical Biology Platform at the Biotechnology Centre Oslo. There he developed the HTS and database infrastructure for a wide range of targets and assay types. It was here he was first exposed to acoustic dispensing technology and immediately saw its utility when used alongside traditional liquid handlers. Now as head of automation at SynbiCITE s Foundry located at Imperial College London, together with his second Access system, he leads a team working on synthetic biology applications, particularly scalable DNA assembly techniques for metabolic pathway engineering, cell free synthetic biology and automated characterisation of bio parts. Marc Emmenegger Ph.D. Student, Institute of Neuropathology, University Hospital Zurich 4:15 PM High-throughput Screenings in Neurodegenerative Diseases Mr. Emmenegger carried out his studies in natural sciences at Lausanne and Zurich University. Having a strong interest in molecular mechanisms underlying neurodegenerative diseases, he joined the laboratory of Prof. Adriano Aguzzi at University Hospital of Zurich as a PhD student. Having established a high-throughput platform, Mr. Emmenegger is currently investigating the role of autoantibodies against proteins known to be involved in neurodegenerative and neuroinflammatory diseases. Dr. Linda D Amore Operational Manager, GeneMill Foundry, University of Liverpool 5:05 PM Challenges and Opportunities for Miniaturization of Workflows in Synthetic Biology Dr. Linda D Amore is the manager of GeneMill, one of the Synthetic Biology foundry in UK. She is a plant biotechnologist and molecular biologist interested in developing next generation sequencing (NGS) methodologies for large construct QC and LIMS system for synthetic biology. During her PhD in plant breeding at the University of Bari (Italy), she studied secondary metabolism pathways in artichoke to isolate gene involved in the synthesis of useful compound for human health. In post-doctoral research at the Centre for Genomic Research in Liverpool (UK), she has generated the data for the wheat genome project In the last 8 years. Dr. D Amore has been involved in optimization of protocols for NGS to improve data quality. She has collaborated with national and multinational companies for the development of instrumental & bioinformatic pipelines to accelerate commercial applications of metagenomics approaches. 8 PROGRAM GUIDE: Labcyte - Edinburgh 2016

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10 LABCYTE EDINBURGH 2016 The Royal Society of Edinburgh Conference Centre, Edinburgh SEPTEMBER, 2016 Synthetic Biology Drug Discovery Single-cell Genomics Dr. Stephan Lorenz Head of Single Cell Genomics Core Facility, Wellcome Trust Sanger Institute 5:35 PM Implementation of Acoustic Dispensing into HT Single Cell Sequencing Workflows After graduating with a Master in Biochemistry at the University of Leipzig, Dr. Stephan Lorenz focused his early scientific career on thyroid adenomas and cancer and the role of calcium signaling in these processes. After completing his PhD in this subject, Dr. Lorenz started to investigate molecular mechanisms of DNA damage in the thyroid as a major contributor to thyroid cancer. This work required him to acquaint himself with Next Generation Sequencing technologies and ultimately led him to join the Wellcome Trust Sanger Institute as a Postdoc dedicated to single cell genomics method development. Since 2013, he has been heading the Single Cell Genomics Core Facility to deliver single cell sequencing as a service to the scientific community and contribute to science by delivering current protocols at scale as well as developing novel applications. Dr. David Simpson Senior Lecturer, Queen s University Belfast 9:40 AM Miniaturisation, Automation and Development of Novel Genomic Applications with Echo 525 and Access System BSc (Hons) in Biological Sciences (1988) and PhD in Molecular microbiology (1995) at the University of Leicester. Several Postdoc positions, a Lectureship, and now a Senior Lecturer at Queen s University Belfast. Dr. David Simpson s group were amongst the first to exploit next generation sequencing (NGS) techniques to screen panels of candidate genes for the inherited retinal disease Retinitis Pigmentosa (RP), characterising patients in Northern Ireland. Another area of interest is the molecular cell biology underlying diabetic vascular complications, specifically the role of micrornas in regulating gene expression in the retina and vasculature. Vesicles released by endothelial stem cells are used to transfer RNAs as a therapeutic for proliferative retinal vascular disease. NGS profiling of small RNAs in model systems and in blood as potential prognostic markers for retinal disease. Currently establishing a genomics core facility, which includes an Echo and Access system, to support and enhance research within Queen s. Dr. Paolo Piazza Section Leader, High Throughput Sequencing Library Prep and Genomics Process Improvement, Wellcome Trust Centre for Human Genetics 10:20 AM Automation Needs for a High Throughput Genomics Facility Dr. Paolo Piazza studied at Universita degli Studi di Milano, where he completed a degree in Biology and a PhD in Genetics. He joined the Department of Plant Sciences, University of Oxford, in 2003 to work on molecular aspects of evolution of plant shapes. Dr. Piazza has been part of the High Throughput Genomics lab since He is currently section leader for the library preparation team and coordinates process improvement initiatives for the core. 10 PROGRAM GUIDE: Labcyte - Edinburgh 2016

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12 Dr. Jani Saarela Operational Manager, FIMM - Institute for Molecular Medicine Finland Synthetic Biology Drug Discovery Single-cell Genomics 11:00 AM RNAi Screening and Cell Based Assay Program at FIMM. The Impact of Acoustic Dispensing to Improve Process Flows Dr. Jani Saarela was educated at University of Helsinki, where he received his Ph.D. in the Medical Faculty in He is currently an operational manager of High Throughput Biomedicine unit in FIMM at University of Helsinki, where he has worked since Before coming to FIMM, Dr. Saarela worked at the National Institute for Health and Welfare, Helsinki, and Medical University of Vienna, Austria. Dr. Andy Breakspear Research Assistant, John Innes Centre, Golden Gate Cloning, Automated Assembly 12:50 PM Recruitment of a Robotic Workforce for Large-scale Construct Assembly Dr. Breakspear is a research assistant on the Engineering Nitrogen Symbiosis for Africa (ENSA) team at the John Innes Centre in Norwich. He manages the DNA synthesis and Golden Gate shared platforms key tools for rapid and reliable construct assembly. As an enthusiastic and passionate teacher, Dr. Breakspear organises Golden Gate workshops designed to provide others with quick and easy access to the technology. Dr. Sunil Chandran Senior Director, Amyris Inc. 1:30 PM High Throughput Platform for strain Optimization and Screening: Reducing the Cost and Time for Commercializing Novel Molecules Dr. Sunil Chandran is a Senior Director in the R&D program management division at Amyris. His primary interests lie in the field of metabolic engineering for the microbial production of chemicals and fuels. While the metabolic engineering community has been extremely successful in commercializing microbial processes, optimization of microbes for economical industrial-scale production of target molecules requires numerous changes to the genetic code of the microbe, which is extremely time-consuming. Dr. Chandran s focus is to accelerate the design-build-test cycle within any strain engineering endeavor by reducing the cost and effort of performing molecular biology while simultaneously increasing throughput. Dr. Tamir Biezuner Research Scientist, Weizmann Institute of Science 2:10 PM A Generic, Cost-effective and Scalable Cell Lineage Analysis Platform Dr. Tamir Biezuner is a Research Scientist at the laboratory of Prof. Ehud Shapiro at the Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Israel. His research focuses on the development of novel tools for single cell genomics analysis. Running the R&D team of the lab, Dr. Biezuner tries to decipher the human cell lineage tree in health and disease using state-of-the-art biochemical protocols, next generation sequencing and laboratory automation. 12 PROGRAM GUIDE: Labcyte - Edinburgh 2016

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15 Echo Liquid Handlers use acoustic energy to transfer DNA oligos and reagents, allowing the reduction of DNA assembly and NGS library preparation reaction volumes. Dramatically reduce reagent costs, save samples, and eliminate steps all while improving the quality and throughput of synthetic genes. 100-fold reduction of Gibson or Golden Gate assembly reaction volumes 100-fold reduction of NGS library preparation volumes Increased assembly and QC throughput Automation to easily process thousands of assemblies Manual Pipetting Echo Liquid Handler Amount of DNA 50 ng ng DNA volume (Rxn) 25 μl 200 nl Library prep volume (Rxn) 25 μl 300 nl Total volume 50 μl 0.5 μl Reactions per kit Cost per reaction $72.91 $0.73 For more information, visit LABCYTE INC. All rights reserved. Labcyte, Echo, and the Labcyte logo are registered trademarks or trademarks of Labcyte Inc., in the U.S. and/or other countries.

16 All product names and brands are properties of their respective owners. LABCYTE INC Borregas Avenue Sunnyvale, CA 94089, USA Toll-free: Fax: Labcyte Inc. All rights reserved. Labcyte, Echo, MicroClime, the Labcyte logo, and Access are registered trademarks or trademarks of Labcyte Inc., in the U.S. and/or other countries. FOR RESEARCH USE ONLY. Not for use in diagnostic procedures. SALES North America Europe info-europe@labcyte.com Japan info-japan@labcyte.com Asia Pacific info-asiapacific@labcyte.com Other info-us@labcyte.com