Advancing Life Sciences

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1 Advancing Life Sciences

2 Sweden s largest center for life sciences A national resource SciLifeLab, Science for Life Laboratory, is a Swedish national center for molecular biosciences, with the mission to develop, use and provide advanced technologies for applications in health and environmental research. National funding makes our services and expertise available to researchers in all of Sweden. The infrastructure is mainly located in Stockholm and Uppsala but we also offer services at other Swedish universities. We offer a cross-disciplinary research setting that interacts with healthcare, authorities and industry to meet the need for new clinical methods and a better environment. In addition, SciLifeLab provides education for students and researchers at all levels. Our technology platforms The SciLifeLab national infrastructure encompasses a multitude of biomolecular technologies and bioinformatics services. On the following pages, we present all current platforms and their associated facilities.

3 Affinity Proteomics Bioimaging Affinity Proteomics offer antibody-based protein analysis and imaging. This includes the investigation of protein properties such as interactions, modifications, expression patterns in tissues, abundance in body fluids and subcellular localization, as well as binding selectivity. These analyses are important for understanding biological processes and disease pathways, as well as to identify and validate new drug targets and diagnostic markers. Biobank Profiling Cell Profiling Fluorescence Tissue Profiling Mass Cytometry PLA Proteomics Protein and Peptide Arrays Tissue Profiling We offer advanced fluorescence microscopy and spectrometry for visualization and quantification on the biological micro- and nanoscale. The Advanced Light Microscopy (ALM) facility has specialized competence and instrumentation for cellular imaging in super-resolution, including 3D-SIM, 3D-PALM/STORM, and 3D-STED microscopy. The Fluorescence Correlation Spectroscopy (FCS) facility offers specialized competence and fluorescence fluctuation instrumentation (FCS, FCCS, RICS, PCH, FRET-FCS) for live cell studies, suitable for monitoring and imaging molecular dynamics and interactions down to a single molecule level. Advanced Light Microscopy hans.blom@scilifelab.se Fluorescence Correlation Spectroscopy stefan.wennmalm@scilifelab.se

4 Chemical Biology Consortium Sweden Chemical Biology Consortium Sweden (CBCS) coordinates, and makes available, powerful infrastructures for the discovery, development and utilization of small molecules for applications in all areas of life science. CBCS provides expertise within assay development, screening, cheminformatics as well as computational, medicinal and enabling chemistry, target identification and compound pharmaceutical profiling. Laboratories for Chemical Biology Umeå (LCBU) The Laboratories for Chemical Biology at Karolinska Institutet (LCBKI) Uppsala Drug Optimization and Pharmaceutical Profiling (UDOPP) CBCS hosts a number of compound collections consisting of both synthetic and natural compounds for biochemical, cellular and phenotypical screening.

5 Drug Discovery and Development We support integrated drug discovery and development projects utilizing the facilities within the platform, which represent a minimal toolbox needed for early drug discovery. Through these we provide industry standard infrastructure, expertise, and strategic support to help progress projects towards a preclinical proof-of-concept. Platform directors Per Arvidsson, Karolinska Institutet per.arvidsson@scilifelab.se Kristian Sandberg, Uppsala University kristian.sandberg@scilifelab.uu.se ADME (Absorption Distribution, Metabolism Excretion) of Therapeutics (UDOPP) Biochemical and Cellular Screening Biophysical Screening and Characterization Human Antibody Therapeutics, Stockholm and U-READ, Lund In Vitro and Systems Pharmacology Medicinal Chemistry Hit2Lead Medicinal Chemistry Lead Identification Protein Expression and Characterization

6 Functional Genomics Metabolomics High throughput methods are transforming basic biological and medical science. It is now possible to apply a holistic perspective and examine all genes and many proteins, their expression, regulation and function in numerous organisms, in any tissue, even at the level of single eukaryotic or prokaryotic cells. Services offered at our facilities include single-cell capture followed by genomic and transcriptomic analysis by next-generation sequencing and protein analysis using proximity-extension, as well as high-throughput screening of extensive sirna and chemical compound libraries in various assays. Eukaryotic Single Cell Genomics sten.linnarsson@ki.se Karolinska High Throughput Center (KHTC) anders.eriksson@ki.se Microbial Single Cell Genomics stebe@ebc.uu.se Single Cell Proteomics caroline.gallant@igp.uu.se The Swedish Metabolomics Centre in Umeå (SMC) provides service in the field of metabolomics using chromatographic techniques in combination with mass spectrometry. SMC offers all analytical steps from sample preparation to data processing, for both untargeted and targeted analysis of small molecules. The service platform works as a professional consultant facility and is divided into two parts; consulting and service. Swedish Metabolomics Centre (SMC) thomas.moritz@slu.se

7 National Bioinformatics Infrastructure Sweden Bioinformatics provides customtailored support beyond the predefined analyses typically offered by the data-generating platforms at SciLifeLab. We offer bioinformatics short-term and long-term support as well as genome annotation service for novel genomes and assistance with data publishing. The platform also provides computing and storage resources for large-scale biological data including know-how, design and implementation of these resources for biological data. Furthermore, we can provide feedback and assistance in experimental planning and design. Bioinformatics Compute and Storage (UPPNEX) Bioinformatics Long-term Support (WABI) Bioinformatics Short-term Support and Infrastructure (BILS) Systems Biology

8 National Genomics Infrastructure The National Genomics Infrastructure (NGI) provides access to technology for massively parallel/ next-generation DNA sequencing and genotyping. Modern genome analyses critically depend on expertise in computational biology, which is closely integrated with NGI to optimize throughput, data handling, and basic analysis. NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center)

9 Next-Generation Diagnostics Structural Biology The aim for the Next-Generation Diagnostics platform is to meet clinical diagnostic needs in health care by providing service and support to promote and adapt the use of high-throughput techniques in routine diagnostics. These technologies include next-generation sequencing, microarray-based analyses and multiplex protein analysis. These have a great potential to impact future set up for clinical diagnostics of cancer, cardiovascular diseases, inherited diseases and communicable diseases, since significantly more information can be provided by these technologies for each patient or sample. Clinical Biomarkers clinicalbiomarkers@scilifelab.uu.se Clinical Genomics valtteri.wirta@scilifelab.se Clinical Sequencing johan.rung@scilifelab.uu.se richard.rosenquist@igp.uu.se Integrative Clinical Genomics tommy.martinsson@gu.se Translational and Clinical Genomics ake.borg@med.lu.se thoas.fioretos@med.lu.se The Structural Biology platform provides expertise and services in the area of biomolecular structure-function-dynamics relationships. Cryo-EM has two sites: one specialized in cryo-tomography and one specialized in single-particle cryo- EM. Both sites have a high-end 300 kv electron microscope, equipped with direct electron detectors. Protein Science provides recombinant protein production and outside the national services also instrumentation for crystallography and biophysical characterization. Swedish NMR Centre provides access to state-of-the-art NMR spectrometers and support for structure/dynamics/interaction analyses of biological macromolecules. Cryo-EM gunnar.von.heijne@scilifelab.se linda.sandblad@umu.se Protein Science helena.berglund@ki.se Swedish NMR Centre (SNC) goran.karlsson@nmr.gu.se

10 Regional facilities of national interest The regional facilities are funded from other sources than the national infrastructure grant. However, these facilities offer service and technologies for researchers in all of Sweden within diverse areas such as bioimaging, array technology, bioinformatics, zebrafish models, biomaterials, mutation analysis and mass spectrometry. Advanced Mass Spectrometry Proteomics Array and Analysis Facility Bioinformatics and Expression Analysis (BEA) Biological Visualization (BioVis) BioMaterial Interactions (BioMat) Clinical Proteomics Mass Spectrometry Mass Spectrometry-based Proteomics, Uppsala Mutation Analysis Facility (MAF) Zebrafish

11 SciLifeLab in numbers Established in 2010 and became a national resource in 2013 Hosted by four universities; Karolinska Institutet, KTH Royal Institute of Technology, Stockholm University and Uppsala University, and collaborates with many other Swedish universities Comprises more than 400 facility employees and 150 research groups Contributed to more than research projects during 2015 Published more than 600 scientific articles in