Facilities
The Netherlands Toxicogenomics Centre will combine the scientific efforts of four well established Dutch toxicological institutions, i.e. RIVM, TNO, RIKILT and Universiteit Maastricht. Hence, fundamental toxicological knowledge, applied aspects of this knowledge and regulatory aspects, all relevant to the establishment of toxicogenomics as a discipline, are covered by NTC at the senior scientist level.

Maastricht University

At Maastricht University, the equipment consists of various spotters and scanners, a complete Affymetrix system, and standard protocols for gene expression analyses. A rat gene bank is available, and mouse and human will soon be implemented (all from Operon). The bioinformatics for DNA microarray applications relies on the BioDiscovery package and in-house build routines in SPSS. Available technologies at the Maastricht Proteomics Centre include protein separation by 1D- and 2D-gel electrophoresis, protein identification by MALDI-TOF (peptide fingerprinting) and LC-Q (peptide sequencing) mass spectrometry.

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TNO Nutrition and Food research

At TNO Nutrition and Food Research, genomics and systems biology programmes have been developed over the recent years.. Apart from the "routine" applications like arraying and 2D-proteomics, TNO's strengths are integrated proteomics and metabolomics (a growing number of NMR, GC-MS and LC-MS platforms). A bioinformatics infrastructure is developed to allow for biological interpretations of data derived from toxicogenomics and nutrigenomics experiments and can be summarized as follows: expertise in testing of various software packages catered towards analysis of microarray data; automated quality control of microarrays (running of in-house written algorithms to generate plots and listings of parameters for quality assessment); extensive expertise in multivariate data analysis of larger datasets from gene expression and metabolome experiments; expertise in the current availablity of and use of pathway analysis/ textmining tools to assist in drawing biologically relevant conclusions from large functional genomics datasets; expertise in datawarehousing.

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Rikilt - Institute of Food Safety

Gene expression analysis DNA arrayers (Biorobotics and Carthesian), scanner for microarrays (Scanarray 2000), PCR/Pipetting robot (MWG), Real-time PCR (Roche Light Cycler), 8-capillary sequencer (Beckman CEQ200), Alf express sequencer, fluorescence and luminescence plate reader, equipment for gelelectrophoresis, various specialised PCR machines, Array image analysis software (Array Vision) and array data-analysis software (Genemath, SPSS), large collection of human- and rat-specific cDNA clones (amongst others from Research Genetics), oligosets for human/rat/mouse (MWG, 10.000 oligo's each) and "home-made" tissue-specific cDNA sets. Proteomics 2D-gelelectrophoresis equipment (IPGphor, Multiphor II, Amersham Pharmacia), imaging software (Imagemaster); LC/MS equipment. MetabolomicsLC-Q TOF-MS, GC-TOF-MS, microLC, LC-MS/MS, GC-MSn, NMR, “home-made" software for analysis LC-MS and NMR data. This software is key in the processing of NMR and MS and is unique in the world. More information on the MS software and its free availability can be obtained via this link.

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RIVM

RIVM has an operational microarray facility with all the necessary equipment. The equipment comprises a Biorobotics spotter, a ScanArray Express scanner, an Agilent BioAnalyzer, and a Nanodrop spectrophotometer. Standard protocols for gene expression analyses are operational, including methods for RNA amplification. Oligo sets for rat (Operon) and mouse (MWG) are available. The bioinformatics includes ArrayVision and GeneMaths/BioNumerics software combined with Splus modules built in-house.

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Wageningen University

Wageningen University has technical expertise on toxicogenomics-based risk-benefit analysis of functional foods and conventional food components, in particular with respect to modulation of cancer risk and endocrine disruption. Wageningen University has broad experience in development, validation and implementation of reporter gene technology-based high-throughput assays and biomarkers for adverse and health-protective effects. Toxicogenomics-related facilities include real-time PCR equipment (I-cycler, BioRad) and FT-MS (orbitrap), 600 MHz LC-SPE-cryoflow NMR-MS (microtof MS) equipment for metabolome analysis. An extensive facility for laboratory animal experiments is also available.

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Leiden University

The toxicogenomics unit of Leiden/Amsterdam Center for Drug Research (LACDR) at Leiden University operates its own Applied Biosystems gene expression microarray platform and has access to Affymetrix microarray platforms. A variety of software is used for image analysis, data visualization, statistical analysis, biological data interpretation, pathway analysis and text mining of array data such as ArrayAssist, Spotfire Decision Site, Rosetta Resolver, GoMiner, BRB-tools, R-packages GSEA, Global test, Limma, and Anni. For automated quality control of Applied Biosystems arrays, custom made software is used.  There are two real-time PCR systems (Roche LightCycler 2.0, MJ Research Opticon 2), an Agilent 2100 BioAnalyzer, an Isogen Nanodrop spectrophotometer and an Applied Biosystems 3100 Avant 8-capillary sequencer. A Palm laser micro dissection microscopy system is also present. For proteomics three GE 2D gelelectrophoresis systems in conjunction with Western blotting equipment are available, in conjunction with a GE Typhoon 9400 gel imaging system and Bio-Rad PDQuest proteomics analysis software. For functional genomics we house a Nikon TE200Epfs four laser confocal microscopy system with a Prior SCAN II automated stage, a controlled heating/CO2 incubator and Total Interference Reflection Fluorescence (TIRF) microscopy and a spectral imaging C1SI unit. ImageProPlus image analysis software is present. For 3D in vitro and in vivo deep tissue imaging a multi-photon Bio-Rad 2100 confocal laser microscopy system is available. Dharmacon siRNA libraries against both human and mouse kinases and phosphatases are present.

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ErasmusMC

At Erasmus MC, the Biosemantics group of the Department of Medical Informatics is developing and validating text mining tools that assist biologists in retrieving, extracting, and relating information and knowledge in the literature and in molecular databases. Research is focussing on the elucidation of hidden or “tacit" knowledge by the massive meta-analysis of textual documents.


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