Our Research Unit has access to several instruments and facilities. Moreover, we have developed and set up a series of analyses during recent years. Interests in collaborations concerning our research competences, facilities and analyses can be directed to the Head of Research or to the responsible employee. Collaboration concerning our routine analyses should be done through contact to “Forskningsservice” (Research Services).
RESEARCH FACILITIES
Responsible employees
- Research Coordinator Pia Søndergaard Jensen, Pia.Soendergaard.Jensen@rsyd.dk,
- Professor Lars Melholt Rasmussen, lars.melholt.rasmussen@rsyd.dk, https://portal.findresearcher.sdu.dk/da/persons/lmrasmussen
Competences and infrastructures
- Many years of experience in building infrastructure for small- and large-scale systematic collection and database registration (biobanking) of tissue and blood–derived material combined with associated clinical data that requires patient consent.Experience with logistical solutions includes both in-house and between hospital projects.
- A comprehensive collection of arterial and adipose tissue (and blood) from more than 5000 clinically well-characterized cardiac and vascular surgery patients
Research equipment
- An inventory management database complying with GDPR
- Zeiss Stemi 2000-C Stereo Microscope
- Leica HistoCore AUTOCUT microtome and Leica HI1210 water bath
Responsible employee
Ass. Professor, Biochemist Louise Helskov Jørgensen
louise.helskov.joergensen@rsyd.dk
Competences
- We can run samples on an automated ELISA platform with which we can provide easy and simple immunoassay testing on many different sample types. We have primarily used tests with kits from different vendors. However, we can easily program the instrument for the use with laboratory-developed assays as well.
- We run most projects in collaboration with external partners. Analyzed molecules have been a variety of species, most often proteins involved in the lipid metabolism, inflammatory markers, etc. We most often use serum or plasma, but we can analyze other sample materials as well.
Research equipment includes
- Triturus (Grifols) automatised ELISA equipment
- ICP-MS (Thermo Fisher)
- ICP-OES (Thermo Fisher)
- Puncher for production of dried blood samples
Responsible employee
Ass. Professor, Biochemist Louise Helskov Jørgensen
louise.helskov.joergensen@rsyd.dk
Competences
We carry out analyses of trace elements in both internal and external projects. We have experience with selenium and a vast number of elements in the “KRAM – Kost Rygning Alder Motion” cohort, where we established new reference intervals. We are currently involved in zinc measurement in projects, where the diagnosis of zinc deficiency is improved. Analyses of trace elements have a very broad applicability, and we can be analyze most elements in all sample types both species-wise and fluid-type.
Research equipment includes
- ICP-MS (Thermo Fisher)
- ICP-OES (Thermo Fisher
- Puncher for production of dried blood spots
Responsible employee
Søren Feddersen, Biochemist, PhD, Associate ProfessorE-mail address: soeren.feddersen@rsyd.dk;Competences
- MicroRNA (miRNA) expression profiling and targeted miRNA expression for clinical applications (biomarker development) using quantitative polymerase chain reaction.
- MiRNA data analysis including identification of reference miRNAs and quantification using different normalization strategies.
- Genetic association studies based on single nucleotide polymorphisms and/or copy number variants.
Sample material includes: Plasma, serum, formalin fixed paraffin embedding tissue samples among others.
Research equipment includes
- ViiA 7 Real-Time polymerase chain reaction (PCR) system with an array card sample block
- Step-One Plus Real-Time PCR system
- LightCycler 480 Real-Time PCR system
- LC-GENIE III
- Next generation sequencing – MiSeq
- QIAsymphony SP
- Maxwell
Responsible employee
Ass. professor Hans Christian Beck, hans.christian.beck@rsyd.dk
Competences
- Sample preparation for clinical proteomics: Body fluids such as Plasma, serum, urine, pleural effusions, etc.
- All kind of tissues including biopsies, sections of formalin-fixed paraffin embedded biopsies, laser micro-dissected samples etc.
- Data analysis, including bioinformatics and biostatistics that also includes clinical variables.
Research equipment includes
- A Thermo Scientific Exploris 480 mass spectromter, and a Thermo Scientific Eclipse Tribrid mass spectrometer – both connected to a Dionex RSLCn-ano LC systems as front end.
- A Dionex RSLC-micro fractionation system for purification and pre-fractionation of peptide samples prior to proteome analysis.
Responsible employee
Ass. professor Martin Overgaard, martin.overgaard@rsyd.dk
Competences
- Targeted proteomics workflows for clinical applications (biomarker development and clinical implementation).
- Sample preparation, using different combinations of biochemical separation strategies such as protein precipitation, size-exclusion chromatography and peptide affinity enrichment using monoclonal antibodies (SISCAPA).
- Sample materials include biobanked plasma/serum, archived dried blood spots, FFPE tissue biopsies as well as other biological specimens in our projects.
Research equipment includes
- Evosep One LC system (Evosep Biosystems) for nano/micro-flow liquid chromatography and integrated sample clean-up interfaced to an EASY-Spray ion source (Thermo Scientific) mounted on a TSQ-Altis QQQ mass spectrometer.
- Automated liquid handling in 96-well format using an Opentrons OT-2 liquid handling robot.
- Datamanagement are performed in Skyline Targeted Mass Spec Environment. Downstream data normalization and biomarker prediction models are performed in various statistical software packages including Stata, Python and R.
Services
Our Department of Clinical Biochemistry (Blodprøver og Biokemi) offers help with blood sampling, analysis of components from our routine repertoire, as well as biobanking to research projects. Researchers that need this help should contact “Forskningsservice” (Research Services).
Responsible employee
Biochemist Palle Fruekilde, Palle.fruekilde@rsyd.dk
Competence
- We carry out analysis of all small molecules, mainly drugs used in TDM (Therapeutic drug monitoring), DOA (Drugs of Abuse), and hormones on a day-to-day basis.
- The most common matrixes within our scoop is plasma, serum and urine, but we are also able to handle other fluids.
- We have more than 20 years’ experience with TDM and small molecules.
- We make tailed, validated methods for specific use.
- We use any available extraction technique to isolate compounds of interest.
- We use LC-MS/MS to detect and quantify compounds.
- We use both 1D and 2D LC techniques.
Research equipment includes
- Five Thermo Scientific high-end TSQ LC-MS/MS (Altis+, Altis, Quantiva)
- Two Hamilton Star pipetting robots for high though-put.
RESEARCH ANALYSES
During recent years, we have developped and set up a series of methods and analyses, used in different projects.
In “Overview of research analyses” you find a short database of these methods. We have separated the database in assays of:
- Single-component immunoassays
- Small Molecules (LC-MS)
- Thrombocyte activity tests
- DNA-sequencing
- DNA-SNP analyses
- Copy number variation
- RNA- and microRNA-expression
- Multiplex proteins (targeted proteomics)
- Discovery proteomics.
Collaborators and examples of publications (PubMed number) are indicated, where relevant.