Infrastructure & Technologies Programme
Oncode stimulates world class oncology research by funding state-of-the-art research equipment & infrastructure across our labs. The Infrastructure & Technologies Programme has a collaborative set-up to make equipment available throughout the community and beyond. Investing in new technologies - which can be used by various researchers and institutions - is one of the ways that Oncode wants to contribute to breakthroughs in cancer research.
The Oncode approach
To extend the current portfolio of available technologies within the community, Oncode invested in technologies and established new facilities, which are available for all Oncode researchers. In addition, Oncode invests in personnel to support researchers to use the technologies and facilities.
Below we have listed the Oncode technologies that are currently available. Oncode researchers can find more information about these via the community platform (please contact firstname.lastname@example.org if you have problems logging in). Non Oncode researchers that are interested can contact email@example.com for more information.
Spinning Disk Confocal Microscope
Location: UMC Utrecht
Contact person: Livio Kleij
Short description: The Spinning Disk Confocal microscope at the UMCU is specifically designed for the imaging of 3D-Cell culture models. Think of organoids, spheroids, zebrafish embryos, or whole organ imaging.
Sequencer Illumina Nextseq 500 Dx
Contact person: Ron Kerkhoven
Short description: The Illumina NextSeq 500 is a next-generation sequencer that can produce up to 120Gb of sequencing data in a single run. The NextSeq enables rapid and cost-effective sequencing of single-cell libraries. Obvious applications are single-cell RNAseq (including T-cell receptor repertoire mapping) and single-cell copy number variation sequencing to chart the inherent heterogeneity present in tumours.
Mass Spectrometer Q Exactive HF-X
Location: Radboud University
Contact person: Pascal Jansen
Short description: The Q Exactive HF-X (Thermo) is a so-called High Field (HF) Orbitrap mass spectrometer, which can be used to measure in depth (phospho)proteomes, sub proteomes of cells, or other biological material of interest. Furthermore, researchers can use this instrument for interaction-proteomics studies, for example to investigate protein-protein or protein-DNA interactions.
BD FACSAria™ Fusion SORP cell sorter
Contact person: Martijn van Baalen
Short description: The BD FACSAria™ Fusion SORP is a 6-laser cell sorter that can be used to identify and isolate specific cell subsets from a heterogeneous sample with up to 18 fluorescent reporters. Four populations can be collected simultaneously, but single cell sorting is also possible. The instrument is located inside a biosafety cabinet and can therefore be used to sort BSL2 class organisms and primary human cells.
Confocal Microscope Leica SP8 AOBS
Location: Erasmus MC
Contact person: Gert van Cappellen
Short description: The Confocal Microscope Leica SP8 AOBS is a DNA damage-dedicated live cell imaging microscope and provides a unique and versatile system capable of inducing virtually all relevant types of DNA lesions. The use of dedicated 266 nm, 355 nm or 405 nm lasers in sub-nuclear areas of living cells, allows to determine the kinetics of multiple DNA damage proteins. DNA damage induction can be automated within the associated operating software.
Contact person: Lennard Voortman
Short description: High speed confocal imaging platform, ideal for high speed live-cell imaging. To enable time-lapse imaging, the system is fully motorized and equipped with an incubation chamber.
Nanostring nCounter® SPRINT
Location: Amsterdam UMC
Contact person: Jan Paul Medema
Short description: The nanostring nCounter SPRINT is an RNA sequencing technology that provides an easy way to screen for a defined set of RNAs at very low quantity without the need for amplification steps. Importantly, also in samples of relatively poor quality (such as formalin-fixed paraffin-embedded (FFPE) tissue), the Nanostring nCounter SPRINT yields reliable data.
Location: Princess Máxima Center
Contact person: Wilbert Vermeij
Short description: The Seahorse XFe24 Analyzer allows researchers to measure a variety of key metabolic parameters and functions in isolated mitochondria, living cells, organoids, cultured human or mouse tissue slices, and fresh patient material. All in a blinded randomized manner in a 24-well format. It can monitor differential functional metabolism between healthy normal tissue and cancers, as well as their responsiveness to therapy and interventions.
Transmission electron microscope
Contact person: Hans Janssen
Short description: This Electron Microscope is mainly used for single particle analysis of protein complexes under cryo-conditions. Researchers can pre-screen complexes under cryo-conditions for purity and homogeneity, collect images to allow 2D-classification, and obtain the initial 3D-models.
Oncode 3D orbital tracking imaging
Contact person: Tineke Lenstra
Short description: With this microscope, the area of interest in a cell can be selected and followed in 3D. This technology makes it possible to follow the location of a specific molecule in time.
Oncode Single-cell (epi) genome sequencing facility
Location: Hubrecht Institute
Contact person: Alexander van Oudenaarden
Short description: This facility supports researchers with DNA analysis at the level of individual cells, both for genomic DNA sequencing as well as epigenetic measurements.
Proteomics for Oncode
Location: UMC Utrecht
Contact person: Boudewijn Burgering and Michiel Vermeulen, Proteomics4Oncode@science.ru.nl
Short description: Diseases such as cancer are characterized by cellular heterogeneity. This facility offers a state-of-the-art single-cell proteomics by measuring the full protein and/or metabolite composition of a single cell.
Oncode GPU infrastructure to enable Artificial Intelligence and Deep Learning applications
Contact person: Anastassis Perrakis
Short description: Research is making more and more use of large and complex data sets that require artificial intelligence for the analysis. With this application, a GPU cluster to be used by researchers is being realized.
Oncode platform for clinical colorectal cancer samples
Contact person: Jelena Medic (Amsterdam UMC)
Short description: This online platform contains all available materials (tissue, blood, residual material) from clinical studies in the field of colorectal cancer that can be used for research purposes. The development of this platform will be completed together with the Prospective National CRC cohort (PLCRC).
Contact person: Anastassis Perrakis
Short description: The Protein Facility will support Oncode researchers with expressing and purifying proteins, characterising them (quality control), and crystallising them for X-ray analysis. This facility can also help researchers measure their interactions with other proteins, nucleic acids, lipids, carbohydrates, and small molecules. Finally, the facility supports in setting up and optimising activity assays.
Oncode Antibody biologics accelerator platform UMAB
Location: UMC Utrecht
Contact persons: Linde Meyaard and Jeanette Leusen
Short description: The goal of this facility is to work closely with researchers to develop new monoclonal antibodies, suited for specific basic research or clinical applications. UMAB employs a new and very efficient cellular immunization method in mice. With this method, antibodies can be raised against for instance low immunogenic membrane proteins. In addition, UMAB can make antibodies against conformational epitopes and generate agonistic and antagonistic antibodies.
The Oncode drug screening centres of expertise in the LUMC and the NKI provide investigators with advice and support to perform compound screens with the Drug Repurposing library. For more information please visit the Drug Repurposing Programme page.