Genome Center Maastricht

                            

 



The Genome Center (GCM) is the research lab for the department of Clinical Genetics of the University Maastricht as well as a Genomics-facility for other research groups in Maastricht and their collaborators. It is funded by the University Maastricht (UM) and by the academic hospital Maastricht (azM). The Genome Center is located on the 5th floor of the UNS50 building (room 5.153) and consists of three basic units:

Head of the Genome Center and general contact person: Bert Smeets

                 1) SNP Genotyping & Sequencing Unit, Supervisor: Jo Vanoevelen

    2) Bioinformatics & Statistical Genetics Unit, Supervisor: Patrick Lindsey

Apart from making instruments and protocols available to the biomedical researchers in the Maastricht area, the Genome Center wishes to point to our expertise in experimental design and data-analysis. In the case of genotyping or expression analysis projects, our experts on biostatistics, bioinformatics, molecular genetics and epidemiology can cooperate with the researcher to maximize the scientific output.

Furthermore, for a number of technologies 3 service levels are available:

     1.       Plug-and-play: Only use of equipment, researcher is responsible for the project. 

2.       Complete support: All/many phases of the project are
     supported by the Genome Center, shared responsibility.

3.       Collaborations : Joint projects.

Below you find an overview of the available technology platforms.

 

 

 


1. Transcription Profiling:


 

Affymetrix Genechip System:


The Affymetrix Genechip system is an integrated platform, containing a hybridisation oven, fluidics station and scanner. Genechips for expression profiling are produced by Affymetrix for a large number of species and contain probes for up to 50.000 transcripts (depending on the species). The probes (>10/transcript) consist of short oligonucleotides, synthesized directly on glass. This results in highly reproducible expression data that can easily be compared with data from other Affymetrix users.

The Genome Center is an Affymetrix Core Lab, which means that all local investigators (UM and azM), as well as their collaborators from institutes outside Maastricht have access to our platform. This also means that we will regularly organize meetings and workshops on experimental design, data analysis and new developments. Data-analysis software licenses can be obtained from the Genome Center.

Overview of available arrays

Finally, the Affymetrix Genechip system can also be used for DNA analysis. For instance, (custom) SNP chips (10K, 100K) or 60 kb resequencing chips can be run on this platform. Please check out the SNP Genotyping & Sequencing Unit below for more information.

 

In-house Microarray Production: Biorobotics Microgrid II


The Biorobotics Microgrid II Arrayer uses 48 pins to acquire sample fluids from up to 24 microplates (384 wells), stored in a cooled biobank. A total of 108 slides, held in place by vacuum, can be arrayed without intervention. The instrument's flexibility allows us to easily tailor the arraying process. A humidifying unit ensures a constant 'printing-climate', essential for the production of reproducible microarrays.

More info on Microgrid II

We now routinely use Corning UltraGAPS slides for the production of expression arrays but other slides can also be used (e.g. for antibody array production). For the development of Ab-arrays we cooperate with the Proteomics Center in the department of Functional Genomics.

cDNA microarrays being produced by the Genome Center involve a 15k mouse embryonic cDNA array (NIA 15k), a 4K heart specific mouse cDNA array and a number of small thematic cDNA microarrays.

Oligoarrays are being produced with 70-mers from Operon. We currently have 3 collections available:

-         5.7k Rat oligo collection v1.1

-         31.7k Mouse oligo collection v3.0

-         21.3k Human oligo collection v2.1

More info on Operon oligos

Arrays are being produced on request. Specific design issues (experimental design, array design) can be discussed with our experts on statistics and bioinformatics.

 

Home-made Microarray Analysis (I): Tecan HS 4800

 

 

The TECAN HS4800 is an automated hybridization system, in which up to 12 microarrays are (pre-) hybridized, washed and dried without intervention.

More info on TECAN HS4800

 

Homemade Microarray Analysis (II): Tecan LS-200

 

 

With this instrument the hybridized arrays are scanned. Up to 4 slides can be loaded into the system, but also other objects within the 96w-format (like 6w-plates, small gels etc) can be scanned. The system is capable of detecting Cy3 and Cy5 signals and generates 16-bit TIFF files that can be analysed with our microarray image-analysis software tools.

More info on TECAN LS200

   


2. SNP Genotyping & Sequencing: 


 

ABI Prism 3730 Genetic Analyser :

 

The ABI 3730 Genetic Analyzer is placed in the ''Noordgebouw'.

Contact: Ellen Lambrichs

 

 

Pyrosequencer PSQ HS 96A:


 

The PSQ HS 96A System is a dedicated medium-throughput SNP analysis platform based on proven Pyrosequencing technology. Up to 96 PCR products are genotyped for known DNA variants (SNPs, InDels, mutations) in about 30 minutes. Because Pyrosequencing is quantitative, allele frequencies can be determined in pooled samples. By testing a short stretch of nucleotides, the system has a built-in QC capability, maximizing precision and reproducibility.

More info on PSQ HS 96A

 

Roche 454 GS FLX System:

 

The Genome Sequencer FLX System, with long-read GS FLX Titanium chemistry, is the flagship 454 Sequencing platform. Offering more than 1 million high-quality reads per run and read lengths of 400 bases, the system is ideally suited for de novo sequencing of whole genomes and transcriptomes of any size, metagenomic characterization of complex samples, resequencing studies and more. The GS FLX System is at the heart of breakthrough scientific discoveries and hundreds of peer-reviewed publications to date.

More info on Roche 454 GS FLX

Contact: Rick Kamps or Iris Boesten

 

 


3. General Equipment:


 

Nucleic Acids Analysis: Nanodrop Spectrophotometer

[NanoDrop]

The Nanodrop is a low-volume spectrophotometer. By using only 1-2 l of the sample, one can measure nucleic acids in a concentration range of 5 ng/l to 3,5 g/l. The device performs a wavelength-scan and will automatically calculate the concentration as well as different ratios. It can also be used for the analysis of Cy-labeled cDNA, to check incorporation efficiencies in microarray experiments.

More info on Nanodrop

Contact: Ellen Lambrichs

 

RNA Analysis: Agilent 2100 Bioanalyzer


This lab-on-a-chip system can analyse up to 12 RNA samples in a matter of minutes. Also, because of the very high sensitivity, extremely small sample sizes (only 1.2 l) can be used. We routinely use the Bioanalyzer to perform a QC on our RNA prior to microarray experiments. Two types of RNAchip can be used: The NANO-chip has a quantitative range from 25-500 ng/l, the PICO-chip analyses RNA concentrations between 0.2-5.0 ng/l.

More info on Bioanalyzer