Accessible research facilities of outstanding quality are vitally important to enable excellent research. The core facilities of the AMC encompass various omics platforms and imaging techniques as well as clinical research facilities. AMC invests in facilities for tissue sampling and storage and in facilities to conduct research according to GLP and GCP standards.
The Bioinformatics Unit has considerable expertise in the design and statistical analysis of linkage and association studies, and in the analysis of SAGE, micro-array and high-throughput proteomics data. It also provides such services as the linkage of various hardware and software applications within the laboratory information management system, and the development of dedicated software applications and analysis tools.
Cellular Imaging Unit
The department of Cell Biology & Histology harbors the central core facility Cellular Imaging, which includes the central flow facility (flow analyzers and cell sorters), advanced fluorescence microscopy (2 Leica SP8 confocals with FRET-FLIM, superresolution, CLEM, upright and inverted wide-field, automated live cell imaging), electron microscopy (scanning and transmission EM, tomography, freeze-fracturing, immune-EM) and a central workstation for data analysis. The facility is part of the van Leeuwenhoek Centre for Advanced Microscopy (LCAM), collaboration between three innovative microscopy centers at the Faculty of Science (FNWI) of the University of Amsterdam, the Netherlands Cancer Institute (NKI), and the AMC.
Clinical Research Unit
The Clinical Research Unit (CRU) was established in 2006 and supports the clinical research in the AMC. The CRU aims to improve the quality of clinical research and ultimately, patient care. The CRU operates according to the Guidelines for Good Clinical Practice (GCP) and in compliance with current regulatory requirements.
- methodological and statistical support to improve the design, conduct, analysis, interpretation, and reporting of clinical research
- methodological support to grant proposals within clinical research
- quality control (monitoring) according to national and international regulatory requirements.
- data management, including randomization applications, web questionnaires and electronic Case Report Forms (eCRFs) development. CRU supports OpenClinica. This open source software allows researchers to build their own eCRF.
The Genomics Unit offers high-throughput (Next generation) DNA and RNA sequencing, as well as several methods for single nucleotide polymorphism detection. The unit is mostly robotized in order to facilitate large expression profiling studies and genetic projects. It also supports the generation and utilization of gene expression arrays and provides DNA and RNA isolation services.Large collections of public microarray data, but also shielded analysis of private microarray dataset(s), can be analyzed via an online genomics analysis and visualization tool, the R2 platform. R2 offers amongst others, analyses such as gene views, differential expression, correlation, survival, genome browsing and pathway analyses. The R2 webserver is freely accessible and intended to be used by biologists, even those with little or no bioinformatics training.
In vivo Optical Imaging Unit
Various optical technologies for in vivo imaging in human subjects and small animals are available in the AMC. Expertise has been built up particularly in the fields of the cardiovascular system and tumour detection, but other areas might be explored as well. Expertise for processing of both clinical and experimental images is available. The primary focus of these technologies is innovative research rather than facilitation.
Medical Imaging Unit
In the AMC the following medical imaging machines are available for research:The AMC participates in the Amsterdam based Spinoza center for neuroimaging (see www.spinozacenter.nl), and a 7T MRI scanner of will be available in 2014 at the Netherlands Institute for Neuroscience (NIN), next to the AMC.
The Metabolomics Unit provides quantitative and qualitative determinations of metabolites in biological matrices. Within the field of metabolomics a dedicated expertise platform for lipidomics has been developed with a focus on lipid composition analysis. The analytical platform comprises UPLC-MS/MS, GCMS, GC and UPLC/HPLC instrumentation including four hyphenated MS/MS systems. There is also a facility for profiling metabolism and bioenergetics in cell lines using the XF96 from Seahorse Bioscience.
The Units serves as well diagnostics of metabolic diseases, personalized patient care, research and development.
The Proteomics Unit is equipped with several mass spectrometers, enabling high-throughput analysis of complicated protein mixtures such as cell extracts or plasma. This set-up was recently expanded with a Synapt G2 mass spectrometer to enable quantitative proteomics using iTRAQ tagging or label-free MSE technology. Consequently, two high-throughput proteomics techniques (iTRAQ and LC-MSE) are available at the AMC .
The radiological facility 'Radionuclide laboratorium' can be used for experiments or diagnostic tests using radioactive labels. The following technologies are available: Gamma counting, Beta counting (vials or 96 Wells format), radioactive labeling experiments, diagnostic RIA kits, cell culture (also ML-I ML-II) using RA labels and cell harvesting, HPLC techniques and in situ labeling.
Medical-technical innovation and development
The Medical-technical innovation and development department (MIO) assists researchers with tailor made technical support. Researchers with an idea or a proposal for a device or with a technical problem within their research are welcome at MIO, together we can look for possible solutions. At MIO we develop and produce single pieces of equipment used for research. The technical support encompasses the mechanical, electronical and software domain. MIO handles projects varying from development of a simple mechanical prototype to large mechatronic devices, and everything in between, such as an adjustable cutting template for heart valve tissue or a transportation device for a bioartificial liver