Genomics and Transcriptomics Core Facilities
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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)

 

 

 

Core Facility Genomics at the Medical University of Vienna

 

The Core Facility Genomics of the Medical University of Vienna operates as a full-service genomics facility providing research scientists and clinicians with services for high throughput analyses of genomes and transcriptomes, in close collaboration with the Biomedical Sequencing Facility of the CeMM / the Austrian Academy of Sciences.
The Core Facility Genomics performes routinely RNA expression profiling and DNA variation analysis of samples of human, mouse and other organisms.
Among others, we operate Illumina technologies for sequencing and Affymetrix GeneChip technologies.
Our services include project design, wet-lab experimental procedures as well as data analysis and help with the interpretation of results.

 

Contact:

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