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EMBL Core Facilities & Service Infrastructure: for you, there & today Vladimír Beneš EMBL Core Facilities & Service Infrastructure: for you, there & today Vladimír Beneš

Core Facilities @ EMBL • Current molecular biology is technology savvy • Funding of Core Facilities @ EMBL • Current molecular biology is technology savvy • Funding of heavy-duty instrumentation is mostly not easy for research groups of the EMBL scale • Economy of centralization enables acquisition of state-ofthe-art equipment • Dedicated, highly qualified staff support scientists in their projects facilitated by frequent & open interactions with users, whose time is ‘limited’, and synergy among CFs • “bottom-up” approach to implementation of new technology to core facilities • Core facilities are also regularly reviewed! • Reasonable prices (strictly non-profit) • Frequently, CFs are the first contact point for the Industry

Core Facilities @ EMBL Heidelberg • • Advanced light microscopy CF (Rainer) Electron microscopy Core Facilities @ EMBL Heidelberg • • Advanced light microscopy CF (Rainer) Electron microscopy CF (Yannick) Protein expression & purification CF (Kim) Proteomics CF (Jeroen, Michail) Flow cytometry CF (Alexis, Malte) Chemical biology CF (Joe) Genomics CF (Vladimir) Metabolomics CF (Theodore)

Advanced light microscopy CF pushing limits of visible light • The first CF, inspiration Advanced light microscopy CF pushing limits of visible light • The first CF, inspiration for the rest; it also set the paradigm for interaction with industry, currently 29 microscope systems • Teaching and support of users throughout the whole process of image data acquisition, analysis and documentation • Development of simplified application Rainer Pepperkok protocols, e. g. by automation, design, set. Rm 506 up, test and offering new equipment in [email protected] de collaboration with industrial partners [email protected] de • si. RNA HT screening libraries

Electron microscopy CF • Teaching sample preparation for EM and operation of EM instruments Electron microscopy CF • Teaching sample preparation for EM and operation of EM instruments to study cell structure and organisation at the EM resolution, including image analysis • Cryogenic methods • EM tomography, immuno-EM • Correlative LM-EM • Whole-cell 3 D imaging Yannick Schwab Rm 310 A yannick. [email protected] de [email protected] de

Protein expression and purification CF • Production and purification of proteins from E. coli, Protein expression and purification CF • Production and purification of proteins from E. coli, insect and mammalian cells • Collection of expression vectors and bacterial strains • Production of enzymes for daily lab work • Biophysical analyses (AUCFG, calorimetry) Kim Remans Rm 303 kim. [email protected] de [email protected] de

Proteomics CF • Infrastructure for identification and characterization of proteins, individual or in complexes Proteomics CF • Infrastructure for identification and characterization of proteins, individual or in complexes • Identification of post-translational modifications • Differential proteome analysis • Steps towards reduction of required input amount thanks to implementation of beads Jeroen Krijgsveld Rm V 213 A jeroen. [email protected] de [email protected] de

Chemical biology CF Joe Lewis Rm 1 D 4. 54 C lewis@embl. de • Chemical biology CF Joe Lewis Rm 1 D 4. 54 C [email protected] de • Interfacing biology with chemistry • Providing academic research groups access to screen small-molecule compound collections against their targets • Identification of novel low molecular weight compounds to use as “biotools” to probe biological function • Characterization of detected interactions • Generating added value IP on in-house targets • Medicinal chemistry, the compound synthesis

Flow cytometry CF • Sorting heterogeneous populations according to many different criteria (cells, chromosomes) Flow cytometry CF • Sorting heterogeneous populations according to many different criteria (cells, chromosomes) into homogeneous populations for experiments • Analysis of single cell populations based on fluorescent probes and light intensities Alexis Gonzalez Rm V 104 [email protected] de

Genomics CF Vladimír Beneš Rm V 106 benes@embl. de genecore@embl. de • Assisting scientists Genomics CF Vladimír Beneš Rm V 106 [email protected] de [email protected] de • Assisting scientists with unlocking genomes of their interest and linking genotype with phenotype • Complete sample processing for: massively parallel sequencing microarrays Fluidigm q. PCR • Single-cell analysis • Full q. PCR support • Assistance with data analysis • Liquid handling lab automation • Fruitfly, nematode, mouse c. DNAs

Metabolomics CF • Global metabolite/metabolomic profiling • Lipidomic analysis • Targeted metabolomic profiling • Metabolomics CF • Global metabolite/metabolomic profiling • Lipidomic analysis • Targeted metabolomic profiling • Metabolite identification • LC-MS development for special applications • Data analysis Theodore Alexandrov Rm 428 theodore. [email protected] de [email protected] de

Contribution to the community: PEPCF-Proteomics CF-Gene. Core project Sequencing of genome and transcriptome of Contribution to the community: PEPCF-Proteomics CF-Gene. Core project Sequencing of genome and transcriptome of Sf 21 & Hi 5 insect cell lines • PEPCF: extensively used in production of eukaryotic recombinant proteins by their expression in baculoviruses but their genomes were unknown • Sf 21 proteins are significant but hitherto non-annotated contaminants in MS analyses • Valuable resource generated Bombyx, 1203 proteins Sf 21, 2427 prot.

The HTX @ EMBL Grenoble Integrated facility for crystallography Jose A. Marquez marquez@embl. fr The HTX @ EMBL Grenoble Integrated facility for crystallography Jose A. Marquez [email protected] fr

Scientific Services Mail-in services with real-time, web access to experimental design and results Nanovolume Scientific Services Mail-in services with real-time, web access to experimental design and results Nanovolume Crystallization platform In Collaboration with the ESRF From Pure samples to Crystals Crystallization screening, Quality control, Crystal Optimisation, Crystal Mounting and cryo cooling. Modes of access: EU Funded (requires application) Integrated Macromolecular Crystallography Service From Pure samples to X-ray diffraction datasets Crystallization, automated crystal mounting and X-ray data collection (ESRF MASSIF). Integrated Compound Screening by MX Full cost Academics Commercial (Industry) Through EMBL-EM Focused libraries (up to 50 compounds) From pure protein to automated ligand screening by MX. Library provided by user Integrated, Fragment Library Screening by MX Fragment libraries (hundreds of fragments/compounds) From pure protein to automated ligand fragment library screening by MX. Library provided by the facility. 14 FP 7 H 2020

EMBL Hamburg Integrated research services in structural biology Computational Services Beamlines Sample Preparation and EMBL Hamburg Integrated research services in structural biology Computational Services Beamlines Sample Preparation and Characterization

Sample Preparation and Characterization Closing the gap between the user home lab and the Sample Preparation and Characterization Closing the gap between the user home lab and the synchrotron Contact: • Helping beamline users from across Europe to prepare and optimize their samples for beamline experiments à optimization protocols à sample characterization à crystallisation trials à quality assessment and quality control Rob Meijers r. [email protected] -hamburg. de

EMBL Beamlines at PETRA III Contacts: P 12 Leading the pack in Small Angle EMBL Beamlines at PETRA III Contacts: P 12 Leading the pack in Small Angle X-ray Scattering P 13 Thomas Schneider t. [email protected] de Longest usable wavelength for crystallography world-wide P 14 Hottest micro-focused beam for crystallography world-wide Dmitri Svergun [email protected] de

Computational Services • remote access to EMBL Hamburg computer cluster • software packages developed Computational Services • remote access to EMBL Hamburg computer cluster • software packages developed at EMBL Hamburg for downloading • access free of charge for academic users From diffraction pattern… …to structure

Summary I. EMBL Core Facilities & Services play a crucial role in enabling scientists Summary I. EMBL Core Facilities & Services play a crucial role in enabling scientists to achieve ambitious research goals Core Facilities & Services are staffed by technology experts who focus entirely on service provision for research projects designed and run by others Emphasis on delivery of quality services, fast reaction times to user demands, reasonable prices Core Facilities’ & Services’ activities are fully driven by EMBL’s scientific agenda Internal surveys have revealed a high level of user satisfaction

Summary II. EMBL Core Facilities are open to Visitors and we provide a lot Summary II. EMBL Core Facilities are open to Visitors and we provide a lot of services to academics in the Member States and even outside The EMBL model for Core Facilities has developed a first-rate reputation in the European sciences community They contribute significantly to internal and external training courses and workshops, often in collaboration with industrial partners. Member States frequently seek our advice and guidance in setting up their own Core Facilities & Services to enhance efficiency and effectiveness of their scientific research For our industry partners, Core Facilities are a clear multiplication factor in terms of business and often a kind of “stamp of approval” for their technologies!

Christian Boulin Fellowships • The fellowships support travel and accommodation cost of young scientists Christian Boulin Fellowships • The fellowships support travel and accommodation cost of young scientists from Member States visiting EMBL Core Facilities to benefit from access to the latest scientific techniques • Funds provided by the Corporate Partnership Programme • 15 fellowships annually, 1500 € each • www. embl. de/services/core_facilities/boulinfellowship/index. html • Email: [email protected] de

Bioinformatics services @ EBI Data and analysis tools for the life sciences www. ebi. Bioinformatics services @ EBI Data and analysis tools for the life sciences www. ebi. ac. uk/services

Key facts about EBI services • • Freely available A comprehensive collection of molecular Key facts about EBI services • • Freely available A comprehensive collection of molecular databases Globally coordinated data collection and dissemination Produced in collaboration with other world leaders, e. g. • NCBI (US) • Wellcome Trust Sanger Institute (UK) • National Institute of Genetics (Japan) • SIB Swiss Institute of Bioinformatics • Cold Spring Harbor Laboratory (US)

Data-driven science, 2000 -2015 More data, more variety, more interdisciplinarity Sequence Human Seq Proteomics Data-driven science, 2000 -2015 More data, more variety, more interdisciplinarity Sequence Human Seq Proteomics Microarray Metabolomics

EMBL-EBI data resources Genes, genomes & variation European Nucleotide Archive 1000 Genomes Ensembl Genomes EMBL-EBI data resources Genes, genomes & variation European Nucleotide Archive 1000 Genomes Ensembl Genomes European Genome-phenome Archive Metagenomics portal Gene, protein & metabolite profiling Array. Expression Atlas Literature & ontologies Metabolights PRIDE Protein seq, families & motifs Europe Pub. Med Central Gene Ontology Experimental Factor Ontology Inter. Pro Pfam Uni. Prot Molecular structures Protein Data Bank in Europe Electron Microscopy Data Bank Chemical biology Ch. EMBL Reactions, interactions & pathways Int. Act Reactome Metabo. Lights Sure. Ch. EMBL Systems Bio. Models Enzyme Portal Bio. Samples Ch. EBI

www. ebi. ac. uk/services www. ebi. ac. uk/services

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Research & Core Facilities @ EMBL Research & Core Facilities @ EMBL

Typical project flow Benchtop assay Research Group Protein Expr. & Purif. CF Flow Cytometry Typical project flow Benchtop assay Research Group Protein Expr. & Purif. CF Flow Cytometry CF Genomics CF Assay development Pilot screen (4 K) 1 -3 weeks Proteomics CF 1 -6 months 1 -2 months Proteomics CF Full screen (80 K) 2 -6 months Cmpd charact. Core Facility Specificity assays Cell based assays Pathway analysis Microarrays, NGS Secondary Assays Research Group In depth biological characterization Med Chem optimisation External Partner

The way to make it work (communication is the key ) Contact CF team The way to make it work (communication is the key ) Contact CF team Discuss your project with CF staff CF helps you with your experiment Analyze and discuss your results with us so that we can learn too please