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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:

Aquatic facility

The LCSB is using zebrafish (Danio rerio) as a vertebrate model organism to study diseases of the central nervous system. The aquatic facility consists of a modern, semi-automated facility that provides husbandry and embryo production services to support biomedical research and teaching activities. Currently, the facility can house up to 30.000 adult zebrafish, offering robotic feeding, maintenance of constant micro-environmental conditions (e.g. pH, temperature and conductivity), and semi-automated cleaning systems that ensure excellent conditions for research quality and animal welfare. Among its services, the Aquatic Facility offers the generation of zebrafish disease models using morpholino antisense technology and CRISPR/Cas9 mutagenesis, as well as pharmacological models and reporter lines using Tol2 transgenesis. Moreover, the platform offers the performance of small molecule screens in zebrafish disease models and reporter lines, as well as toxicity screens for drug safety assessment. So far, around 10 international investigators have been trained in our facility to successfully use zebrafish in their research, and implement technologies in their host institutions.

For any questions, do not hesitate to contact the aquatic facility via email.

Rodent facility

The rodent facility has been established to assist researchers in the development and analysis of various in vivo models including humanized and germ-free animals. The facility has the capacity to house more than 100 different mouse lines in 1500 IVC cages in the Breeding barrier under SOPF status. The Experimental barrier with a capacity for 600 mouse and 300 rat cages, is dedicated to studies on transgenic rodents and offers as well the possibility to realize BSL-2 activities and housing xenograft models. Genetically modified rodent lines can be generated by our Transgenic Core Unit and kept either as live animals or as cryopreserved sperm. The facility offers the possibility of running a broad number of experimental procedures on the premises, including stereotaxic surgical procedures and motor behavior equipment as the Catwalk. Additionally, humanized mouse models can be provided within an SPF environment. The Germ-free Unit is established within the Breeding barrier to ensure a controlled health status. For colonization studies, germ-free mice can be inoculated with a suspension of a specific microbe (mono-colonization), a defined finite group of microbes, or a polymicrobial mixture. This unit also employs a Sealed Positive Pressure IVC system to achieve the type of germ-controlled environment.

For any questions, do not hesitate to contact the mouse facility via email.

Sequencing Platform

The sequencing platform at the LCSB offers next-generation sequencing services. The platform has a NextSeq500 and a MiSeq sequencer from Illumina and a MinION nanopore sequencer from Oxford Nanopore Technologies. The Illumina sequencers allow sequencing read lengths from 50 bases to upto 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, library preparation, library quality control, sequencing run, raw data generation and preliminary data quality control report is performed. General applications include RNA sequencing, metatranscriptomics, single cell RNA sequencing, metagenomics, small genome sequencing, ChIP sequencing, DNase I sequencing, ATAC 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.

For any questions, do not hesitate to contact the sequencing platform via email.

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, Sciex 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.

For any questions, do not hesitate to contact the metabolomics and mass spectrometry platform via email.

Bioinformatics Platform

The LCSB Bioinformatics Core offers large data storage as well as bioinformatics expertise, which includes state-of-the-art workflows for data capture and data analysis using OpenStack based private cloud as well as high-performance computing (HPC) cluster of the University. In 2016, the core facility group has been made the Luxembourgish Node of the European bioinformatics infrastructure ELIXIR and serves as an international data hub for clinical and translational medicine data (see Flagship projects page 21). 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 dynamic visual analysis workflows and libraries (e.g. Fractalis) based on machine learning approaches and tools (e.g. ADA) for the integration of heterogeneous data across different data types and disciplines. Visualisation is supported by virtual and augmented reality, as well as disease map approaches, such as the PD map (see Flagship projects). Easy tools provided by the Bioinformatics team allow researchers to set up and fill their own disease map. 

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). In addition, two super-resolution light microscopy approaches were recently established: a 3d STED microscope (Leica SP8) and the Rescan module (confocal.nl). Technologies are used for the study of fixed and living cells and tissues with genetic or pharmacological perturbations, 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. Currently a Scanning Electron Microscope (Zeiss Sigma 500) is being built up and will be available in 2019.

For any questions, do not hesitate to contact the imaging platform via email.