Genome Center Maastricht
The Genome Center (GCM) is the research lab for the departments of Population Genetics and 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)
Transcription Profiling Unit, Supervisor: Torik
Ayoubi
2)
SNP Genotyping & Sequencing Unit, Supervisor::
Bert Smeets
3)
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 we will give 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.
à Overview
of available arrays
Contact: Torik
Ayoubi
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.
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
Arrays are being produced on request. Specific design issues (experimental design, array design) can be discussed with our experts on statistics and bioinformatics.
Contact: Torik Ayoubi / Erika Timmer
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.
Contact: Torik Ayoubi / Erika Timmer
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.
Contact: Torik
Ayoubi / Erika Timmer
2. SNP Genotyping &
Sequencing:
ABI Prism 3100 Genetic Analyser
:
The ABI3100 Genetic Analyzer is a multi-color fluorescence-based DNA analysis system using capillary electrophoresis with 16 capillaries operating in parallel. The 3100 Genetic Analyzer is fully automated from sample loading to data analysis. Applications are in the fields of DNA-sequencing, multiplex SNP-detection (SNaPshot, Single Base Extension) and fragment analysis (Genome scans, LOH studies, fluorescent RFLP). Sequencing and Genescan throughput is 16 samples/hour; multiplex SNaPshot throughput is 32 samples/hour. The system can (fully automatically) handle up to 768 samples without intervention.
à More info on ABI3100 Genetic Analyzer
Contact: Ellen Lambrichs/Frank Beijers
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.
Affymetrix Megallele System
:
The
Affymetrix Megallele system is an integrated platform, containing a
hybridisation oven, fluidics station and scanner. With the Megallele system, we
are able to accommodate the current Affy 10K and 100K SNP chips as well as the
500K SNP chips that will be launched by the end of 2005. Furthermore, it is now
possible to design and analyse your own custom SNP chips containing up to 10.000
custom SNPs. Finally, resequencing chips are also available on which 30kb of
sequence can be analysed in both directions. We already have the MitoChip
operational, on which the mtDNA is present in duplicate.
à Overview
of available Affy SNP and resequencing arrays
à Overview
of available Megallele custom SNP arrays
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.
Contact: Bert Smeets
3. General Equipment:
Nucleic Acids Analysis: Nanodrop
Spectrophotometer
![[NanoDrop]](../stylesheets_unimaas_nl/genome12.jpg)
The Nanodrop is a
low-volume spectrophotometer. By using only 1-2 µl of the sample, one can
measure nucleic acids in a concentration range of 5 ng/µl to 3,5 µg/µl. 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.
Contact: Ellen Lambrichs/Frank Beijers
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 µl) 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/µl, the PICO-chip analyses RNA concentrations between 0.2-5.0 ng/µl.
Contact: Torik
Ayoubi / Erika
Timmer
Automated Liquid Handling &
PCR: Tecan Genesis RSP 150 system with Biometra Trobot cycler
We have a robot liquid
handler operational for automated PCR setup. The platform is
equipped with 4 'vari-span' pipetting-channels (disposable tips). The
liquid handler has an integrated Biometra Trobot thermal-cycler for automated
PCR. Also, sample tracking is possible by using the integrated barcode scanner.
Cooled pipetting and storage positions ensure enzyme stability and prevent
evaporation.
à More
info on Tecan liquid handlers
