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Expertise centers
Expertise centers

The CMM houses experts and state-of-the-art facilities for a broad range of techniques. Below you'll find a description of the scope and services of the Expertise Centers as well as contactpersons.

UTRECHT SEQUENCING FACILITY

Coordinator:                           Ies Nijman
Website address:                   www.USEQ.nl
Contact:                                   USF@umcutrecht.nl / +31 88 - 75 68204

Scope of Expertise Center 

To facilitate Next-generation sequencing applications by using state-of-the-art technology, provide expertise knowledge for experimental design and data analysis, and make new DNA/RNA characterisation techniques available.

Services

Consultancy and knowledge transfer

The facility has a weekly consulting hour on Friday to advise on experimental design, technology, and library preparation choice, data analysis and follow-up experiments. Please inform us upfront on the topic by email (USF@umcutrecht.nl).

Sequencing

The facility provides sequencing of ready to run samples or samples that need to be isolated and/or library prepped by the facility. The facility operates a broad range of sequencing equipment:
- Illumina MiniSeq, Miseq, NextSeq, HiSeq
- Oxford Nanopore single molecule sequencing
In addition, we provide access to Whole Genome Sequencing at our partner institute Hartwig Medical Foundation.

DNA/RNA isolation

The facility offers automated DNA/RNA isolation of whole tissue, cells, organoids, blood and other body fluids, obtaining the high quality needed for NGS sample prep or fingerprinting.

Sample preparation

The facility offers to convert isolated DNA/RNA samples into NGS libraries that are ready to sequence.

SNP fingerprinting

The facility offers to do standardized panel-based SNP typing on DNA samples to detect potential sample swaps.

Microscopy

Name of Expertise Center:  Cell Microscopy Core
Coordinator:                            George Posthuma
Website address:                    http://www.cellbiology-utrecht.nl/facilities/cell-microscopy-core.html
Contact:                                    +31 88 75 56548

Scope of Expertise Center: The CMC facilitates clients to apply standard and specialized light microscopy (LM) and electron microscopy (EM) methods. The LM techniques are confocal and wide-field with set up for live cell imaging. The EM techniques are transmissionEM (TEM), 3D tomography and focused ion beam scanningEM (FIB.SEM). The signature technique of the CMC is immunoTEM (immunogold labeling of cryosections; the so called Tokuyasu technique). The power of the CMC lies in integrating LM and EM images via correlative light – electron microscopy (CLEM). The CMC takes an internationally leading position herein by correlation of Tokuyasu sections from LM to EM and by developing correlative live cell to 3D EM protocols.

Services: The CMC provides 3 types of services:
• A short (pilot) study (no fees): specimen preparation and further interpretation of results are done by CMC personnel. On average such a project should not take more than 40 hr.
• Access to equipment (cost prize). If a research question requires more than 40 hr the client can provide personnel that is trained to perform the experiments at the CMC. Clients receive guidance during all aspects of their project(s) by the site personnel (free of charge). After thorough instruction the client has access to the equipment and pays a fee for the use of the equipment.
• A collaboration (no fees)

In all cases the CMC staff advises on the experimental design.

Cell screening

Name of Expertise Center:  Cell Screening Core (CSC)
Coordinator:                             David Egan
Website address:                     http://www.cellbiology-utrecht.nl/facilities
                                                    /cell-screening-core.html

Contact:                                     d.a.egan@umcutrecht.nl / +31 88 7568 219

Scope/services of Expertise Center: The Cell Screening Core, (CSC), at the Department of Cell Biology of the UMC Utrecht, is a well-established core for high-throughput screening. The Core has an automated high-throughput cell screening system in use since 2009. This platform is designed to allow biomedical researchers to screen a variety of siRNA and compound libraries in 96- and 384-well plates. Research has concentrated to a great extent on the use of high content screens that utilize automated microscopy, thus leveraging the extensive experience in fluorescence light microscopy present within the department in the form of the Cell Microscopy Core. The various projects run at the CSC address important biomedical research areas including cancer, neurological diseases, childhood diseases and stem cell biology, which are defined focus areas, ('speerpunten') within the UMC Utrecht.


 

Structural Biology

Name of Expertise Center:  Structural Biology
Coordinator:                            Holger Rehmann
Website address:                    -
Contact:                                    h.rehmann@umcutrecht.nl / +31 88 7568 961

Scope/services of Expertise Center: 
To enable researchers within the UMCU connecting their research with available information on protein structures and identifying strategies for the implementation of approaches driven by structural biology.
Questions could be (but are not limited to): What are the structural consequences of a mutation I identified in a patient? How does a drug interact with its receptor? How to design an optimal construct for protein expression? How to create a catalytic dead mutant? How can I get a figure from a pdb file?
We wish to offer low-threshold contact.

 

 

Proteomics

Name of Expertise Center:  proteomics@umcu
Coordinator:                            Harmjan Vos
Website address:                     -
Contact:                                    proteomics@umcutrecht.nl / +31 88 75 68129

Scope of Expertise Center: The proteomics facility will provide state-of-the-art proteomics methods to aid fundamental, translational and clinical research into proteins, protein modifications and biomarkers relevant for health and disease.

Services:
New users: Together with the investigator we design a strategy, give advice on technical experimental details, provide specific reagents, process the sample according to the chosen strategy, measure the sample, process the raw data and analyze the output. Output is discussed with the investigator and further options are considered.

Experienced users: Dependent on the level of experience of the investigator above mentioned steps can be omitted. Ideally, after the strategy discussion, the investigator prepares ready to run samples, raw data is processed, output is analyzed and discussed together.

 

 

Metabolomics

Name of Expertise Center:  Metabolomics
Coordinator:                            Boudewijn Burgering/Nanda Verhoeven
Website address:                     -
Contact:                                    B.M.T.Burgering@umcutrecht.nl /
                                                   +31 88 7568918  or
                                                   N.Verhoeven@umcutrecht.nl /
                                                   +31 88 75 553 17

Scope of Expertise Center:  The Utrecht Center for Medical Metabolomics unites metabolic knowledge from both the diagnostic laboratory and more fundamental metabolic research. We offer a wide range of analyses for biomedical research and have a great number of collaborations, within and outside the UMCU to study metabolism in the context of their – research – question. Services may range from providing theoretical background to understand contribution of metabolism in biological phenomena to providing multi-scale large number analytical analysis of metabolites in biological samples.

Services: Various mass-spectrometry based approaches towards metabolite identification and/or quantification. Targeted metabolomics in body fluids, cells and tissues (LC-MS/MS, GC-MS). Untargeted metabolomics (mass spectrometry, direct infusion, exact mass) Seahorse technology. Several platforms are operational for dedicated analysis of metabolites (see also http://www.umcutrecht.nl/nl/Ziekenhuis/Professionals/Diagnostiek-aanvragen/metabole-diagnostiek) and depending on the research question a platform for measuring a dedicated metabolite/group of metabolites can be developed.
All involvement of this facility is determined through an initial intake meeting to discuss feasibility and practical issues such as possible sample fee, potential co-authorship etc. For contact see above.

 

 

Bioinformatics

Name of Expertise Center:  Bioinformatics
Coordinator:                            Joep de Ligt
Website address:                    www.ubec.nl
Contact:                                    j.deligt@umcutrecht.nl / +31 88 75 68082

Scope/services of Expertise Center: 
The mission of the UBEC is to facilitate CMM and affiliated researchers in transforming their data into insight. This will be achieved by delivering:
● outsourcing services for taking over routine and standardized data analyses and data stewardship
● helpdesk and support services on bioinformatics and compute questions
● consulting on advanced data analytics, high-performance computing and data stewardship
● data stewardship
● grant application support for data analytics and data stewardship
● harmonizing bioinformatics expertise between researchers - especially between embedded bioinformaticians - by hosting regular, topical, bioinformatics meetings as well as alignment of bioinformatics projects to increase productivity.
● innovation of the in-house bioinformatics expertise and introduction of new tools and methods
● education on bioinformatics, data analytics and data stewardship in the BSc and MSc programs of the CMM
● HPC technical and scientific coordination.

 

 

iPS

Name of Expertise Center:  Induced pluripotent stem cell facility
Coordinator:                            Koen Braat
Website address:                    http://www.cellbiology-utrecht.nl/
                                                   facilities/ipsc-facility.html

Contact:                                    k.braat@umcutrecht.nl / +31 88 75 56474 or +31(0)88 75 56477

Scope of Expertise Center: 
Generation of induced pluripotent stem cells, sharing expertise and supply support.

Services:
Consultancy and expertise
The facility provides expertise on iPSC culture, differentiation (if knowledge is available), basic characterization.

iPSC generation
Generation of iPSC from several cell sources using a polycistronic lentivirus or a non-integrative plasmid system. Alternative (non-integrative) reprogramming methods are planned for the future.

 

 

Organoids

Name of Expertise Center:  Organoid expertise center
Coordinator:                            Hugo Snippert
Website address:                    -
Contact:                                    h.snippert@umcutrecht.nl / +31 88 75 68 989 (secr.)

Scope/services of Expertise Center: 
Consultancy and knowledge transfer
To provide expertise knowledge for experimental design and Q&A to researchers within the UMCU who are interested in working with mouse or human organoids cultures.
We provide a monthly consultancy hour on the first Friday of the month to advice on experimental design, technology, platform choice and experimental details. The center is able to facilitate connections with the right experts (culture/ drug screening/ microscopy/ CRISPR) from any of the participating labs, depending on the topic.
Time slot: First Friday of the month, between 14:45h-15:45h.