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Bioinformatics in Austria! (2015-04-14T08:43:53.062+02:00)
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Genomics and Transcriptomics at the University of Veterinary Medicine Vienna

 

The Core Facility Genomics & Transcriptomics at the University of Veterinary Medicine Vienna focuses on the design and accurate measurement of quantitative experiments targeting DNA and RNA (mRNA to miRNA) sequences.Sample (pre)processing, for example by separating single cells using fluorescence activated cell sorting and by laser capture micro-dissection (LCM) to facilitate selective sampling of individual cells or groups of cells from histological specimens, represents a special field of expertise. The amplification refractory mutation system (ARMS)-qPCR is a key method to quantify mixtures of SNP sequences. The facility offers the opportunity to run digital PCR to accomplish more accurate quantification compared to qPCR. Quantification of nucleic acid sequences can be performed by RT-qPCR (in house) or by several next-generation sequencing approaches (outsourced to external providers).

Contacts:

Ralf Steinborn ralf.steinborn@vetmeduni.ac.at

Reinhard Ertl reinhard.ertl@vetmeduni.ac.at

 

 

Genomics and Transcriptomics at the MUI

Sequencing & Genotyping Core Facility

The Sequencing & Genotyping Core Facility of the Innsbruck Medical University focuses on high throughput DNA sample processing, SNP genotyping, real-time PCR, Sanger sequencing and analysis of mitochondrial DNA using both Sanger and next-generation sequencing. Sanger sequencing and fragments analysis applications are performed on an ABI 3130xl (16 capillaries; medium throughput) and a ABI 3730s (48 capillaries; compatible with both 96 and 384 well plates for high throughput). TECAN robots with either 8 pipetting channels or 96 channels are available for automated DNA sample normalization and high-throughput processing of 96 well or 384 well plates. SNP genotyping can be performed either on an ABI QuantStudio 6 Real-Time PCR system for low-throughput singleplex applications or an Agena (formerly Sequenom) MassARRAY4 DNA MALDI-TOF system for large scale multiplexed genotyping. The Agena system is able to genotype up to 35 SNPs per sample and is operated in a 384-well format allowing the generation of more than 100.000 genotypes per day.

Besides genotyping, the MassARRAY system can be used also for highly sensitive detection of somatic mutations (leveraging the high sensitivity of MALDI-TOF detection), quantification of DNA Methylation (Epityper) and DNA-based blood group typing (HemoID). For somatic mutation detection in cancers also some ready-to-use panels are already available at Agena Bioscience (http://agenabio.com/genetics), such as OncoCarta for solid tumours or melanoms, OncoFocus for lung, colorectal and metastatic melanoma, LungCarta for lung adenocarcinomas and LungFusion for the detection of fusions in ALK, RET, or ROS1 (sensitivity for all is about 5-10%). For very rare somatic variants, strepatividin-biotin capturing of the rare variant can be performed, allowing a detection sensitivity of <1% (UltraSeek)

Additional equipment available includes an AATI Fragment Analyzer system for cost effective quality control of NGS libraries, an Qiagen EZ1 DNA extraction robot and an TECAN  Infinite® 200 PRO multimode plate reader for DNA quantification in microwell plates or in low volumes (2 µl) using a NanoQuant plate.

Contacts: Website Core Facility  Website Insitute

Florian Kronenberg (Florian.Kronenberg@i-med.ac.at)

Stefan Coassin (Stefan.Coassin@i-med.ac.at)

 

Global gene analysis at the Medical University of Vienna

 

The Medical University of Vienna Core Facility Genomics operates as a full-service genomics facility providing research scientists and clinicians with services for RNA expression profiling and DNA variation analysis. Technologies offered through the Core Facility include an Affymterix GeneChip microarray platform and a Illumina HiSeq2000 Next generation sequencing instrument amongst others. Services may include project planning, lab experiments, data analysis, and interpretation.

Contact
Assoc.-Prof. Priv.-Doz. Mag. Dr.Martin Bilban
email: martin.bilban@meduniwien.ac.at

phone: + 43 (0)1 40400 - 73539

Univ.-Prof. Dr. Berthold Streubel
email: berthold.streubel@meduniwien.ac.at
phone: +43 (0)1 40400 - 2819

Dr. Christoph Bock
CeMM Principal Investigator
email: cbock@cemm.oeaw.ac.at

phone.: +43 (0)1 40160 - 70070

 

http://corefacilities.meduniwien.ac.at/genomics/

 

 

 

Genomics and Transcriptomics at the AIT 

 

 

The Business Unit Molecular Diagnostics at the AIT Austrian Institute of Technology focuses on the discovery and validation of biomarkers suitable for minimally invasive disease diagnosis – and/or prognosis from body fluids. Beside serum - and plasma-based diagnostic assay development the research group recently has a special interest in saliva diagnostics thereby focusing in particular on DNA-methylation-, micro-RNA - and autoantibody-based biomarkers. AIT’s technological expertise comprises the isolation of the whole variety of biomolecules from minimal amounts of sample material (e.g. biopsies, FFPE specimens , body fluids) as well as the profiling, discovery and validation of DNA-, mRNA/microRNA-, protein– or autoantibody-based biomarkers using various state-of-the-art high throughput technologies.

 

Devices:

1)    Ion Torrent PGM & access to Ion Proton (NextGen Sequencing)

2)    LightCycler 480 (real-time PCR)

3)    Biomark Fluidigm (real-time PCR)

4)    Agilent Scanner & Bioanalyzer (Microarray platforms)

5)    AIT 16k protein- & 170k peptide array (Microarray platforms)

6)    Luminex FlexMap3D (Multiplexing platform)

 

AIT’s research services further include the design and development of bio(marker) assays. Read more…

 

Contacts:

Andreas Weinhäusel andreas.weinhaeusel@ait.ac.at

Christa Nöhammer christa.noehammer@ait.ac.at

Genomics & Transcriptomics at the BOKU

 

The Extremophile Center Core Facility is specialized on a group of fungi, which are small, black and strong:  "Black yeasts" and "Microcolonial fungi" resist extreme situations; the UV-radiation and dehydration in desert just like the radioactivity or extreme ozone pollution.

We examine the molecular and cellular mechanisms of stress resistance in fungi and other microorganisms with the aim to make them useful for biotechnological applications.

 

Our research aims to have biotechnological applications:

  • Development of antioxidants and other cell-protectants for medical and cosmetic applications in relation to UV-stress and free radicals as well as in terms of application in radiotherapy.
  • Development of novel anti-fungal therapies.
  • Biotechnological use of novel degradation processes for biological purification of waste gases (biofilter), water and soil as well as the bioconversion of pollutants and other waste products into usable energy resources.
  • The optimization of fermentation process by increasing the resistance of the producer-strains.

 

Equipment

 

  • ION Proton™ - Benchtop Next Generation Sequencing
  • ION PGM™ System
  • Environment Emulation System - EES 4667
  • Parallel Bioreactor System
  • TGA/DSC (Thermal Gravimetric Analysis /Differential Scanning Calorimetry)

 

You find more detailed information about our facilities and services here: http://eq-vibt.boku.ac.at

 

Contact:

Ingrid Döller-Diem

Tel.: +43 (0)1 47654-99304

Email: ingrid.doeller-diem@boku.ac.at

Genomics and Transcriptomics at the Medical University Graz

 

 

The Core Facility Molecular Biology at the Medical University Graz focuses on Microbiome analysis by 16s amplicon based sequencing as well as on de novo and re-sequencing of small genomes on the MiSeq Illumina Next Generation Sequencing platform. Implementation of 16s analysis for clinical applications is on high priority of the group but the analysis from a variety of human, animal and environmental sample material is possible. The workflow offers automated DNA isolation, amplification of hypervariable regions, library preparation, sequencing and basic data analysis. Further, the Core Facility is very well experienced in gene expression analysis by the Affymetrix GeneChip® array hybridization system, qRT-PCR and the nCounter® Analysis System. The Affymetrix platform offers a highly reproducible whole transcriptome screening method and generated data are analyzed in the Partek® Genomics Suite software. Nanostring complements our technologies by digital counting of RNA and DNA molecules without the need of reverse transcription and amplification. For advanced data and pathway analysis the Ingenuity Pathway Analysis software IPA is available in the Core Facility

Contact: Ingeborg Klymiuk (ingeborg.klymiuk@medunigraz.at)


 

Core Facility Molecular Biology Graz

[[Genomics_and_Transcriptomics_at_the_University_of_Veterinary_Medicine_Vienna]]

[[Genomics and Transcriptomics at the AIT]]

[[Genomics and Transcriptomics at the MUI]]

[[Core Facility Genomics at Medical University of Vienna]]

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