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Cutting across disciplines in systems biomedicine, the LCSB integrates different technologies, models and expertise; from mathematical theory to practical medical requirements of the clinic. This allows the centre to adapt in the best possible way to the challenges of modern biomedical research. The goal of the LCSB is to establish and provide access to important infrastructure that supports the key research lines of the LCSB.

Larger infrastructure is established as ‘central platforms’ to make it easily accessible across all research groups, and to offer fee based services at national and international level. Besides offering customised services and method development, central platforms organise training workshops on new technologies, offer consultation for experimental design, data processing and troubleshooting. So far, the LCSB has established the following central platforms:

Mouse facility

Currently a small Specific Pathogen Free (SPF) rodent facility that accommodates up to 420 cages for breeding, cohort generation and experiments is available to the LCSB and the Life Science Research Unit at the University. Because of the availability of transgenic models and the wealth of well-established experimental procedures, this facility is a resource for research on neurodegenerative diseases and cancer. The facility offers a rodent breeding service, including the management of the mouse colony as well as additional services for generating transgenic animals. A new animal facility is currently under construction and will open its doors at the end of 2017. The new facility offers space for 1500 rodent cages, separated in SOPF breeding areas and SPF experimental units. All facilities offer constant maintenance of micro-environmental conditions to ensure animal welfare.

Sequencing platform

The sequencing platform at the LCSB opened end of 2016, and offers next-generation sequencing services. The platform has currently two sequencers, a NextSeq500 and a MiSeq from Illumina and a MinION nanopore sequencer from Oxford Nanopore Technologies. The Illumina sequencers allow sequencing tunable read lengths up to 300 bases of single- as well as paired-end runs while the MinION sequencer complements by ultra-long read lengths (up to several hundreds of kilobases). Together this offers high flexibility for the different sequencing needs. The platform offers full service, starting with advice in experimental design up to sequencing data generation. Receiving RNA or DNA samples, sample quality check, sample shearing, library preparation, sequencing run, raw data generation and preliminary data quality control report is performed. General applications include RNA sequencing, metagenomics, small genome sequencing, targeted gene sequencing, amplicon sequencing, and HLA typing. Furthermore, upon user request, the sequencing platform works closely with the ‘bioinformatics platform’ to offer downstream data analysis. Besides the wide range of standard services, the platform also offers new method development.

Metabolomics and Mass Spectrometry platform

The Metabolomics Platform offers both GC-MS and LC-MS services, access to equipment for sample preparation and a comprehensive set of tools for reliable data analysis based on a statistical evaluation. Moreover, to address the needs in this fast changing field, the Metabolomics Platform continuously develops new analytical and tailor-made methods to address upcoming biological and biomedical questions. This includes targeted and non-targeted GC-MS as well as LC-MS analyses, semi-quantification and absolute quantification of metabolites extracted from several sample types, including mammalian cells, bacteria, yeast, body fluids and soft tissues. The platform hosts three cutting-edge LC-MS systems (Agilent 6560 Ion Mobility Q-TOF, Thermo Q Exactive, ABSciex Q-Trap) and two Agilent GC–MS served by multifunctional sample preparation robots. Using these state-of-the-art technologies and standardised laboratory protocols, the Metabolomics Platform strives to offer high quality mass spectrometry-based measurements of a wide range of small molecules in biologically relevant samples.

Bioinformatics platform

The LCSB Bioinformatics Core is the Luxembourgish Node of the European bioinformatics infrastructure ELIXIR and serves as an international data hub for translational medicine data that comprises clinical, molecular and experimental data to create sustainability and accessibility around this data for further research. The hosting of this data is accompanied by data access management as well as analysis and compute facilities based on the infrastructure of the high performance computing cluster of the University. The bioinformatics platform further assists in the curation of existing clinical data for computational analysis, introducing international standards and performing quality control of entries. Support is given for the development of electronic data capture based on controlled vocabulary in CDISC standards and their storage in suitable tools for analysis such as tranSMART. A powerful genome analysis pipeline interprets data from exome and whole genome data while other bioinformatics tools have been developed to interpret differentially expressed genes within pathways and networks. The Bioinformatics Core further develops advanced analysis workflows based on machine learning approaches and tools for the integration of heterogeneous data across different data types and disciplines. Visualisation is supported by virtual reality and disease map approaches. The PD Map is a resource that allows researchers to map their data on the existing curated literature around Parkinson’s. Easy tools provided by the platform allow also researchers to set up and fill their own disease maps.

Imaging platform

The imaging platform offers of a broad palette of microscopy systems: a laser scanning confocal microscope (Zeiss LSM 710) for high-resolution imaging of fixed samples, a spinning-disk confocal microscope (Zeiss Cell Observer) and an inverted epifluorescence microscope (Nikon Eclipse Ti-E) for prolonged live-cell imaging, a selective plane illumination microscope (SPIM) for low phototoxicity whole organ and organism imaging, as well as a high-content screening system (Perkin Elmer Opera). A new super-resolution fluorescence microscope (based on the STED principle) will soon be integrated to the platform. Technologies are used for the study of fixed and living cells and tissues with genetic or pharmacological perturbation, followed by sophisticated image analysis of cell morphology, topology and cellular dynamics. Furthermore, the facility comprises a flow cytometry branch with a cell sorter (BD FACSAriaIII) and high-speed analyser (BD LSRFortessa) allowing quantifying of large cell populations at single cell resolution and performing a variety of high-throughput assays and phenotypic selections. User trainings take place throughout the year through practical courses, seminars and workshops.