Transcriptomics

 

Next generation sequencing

Next generation sequencing (NGS) is a novel high throughput technology for RNA / DNA based research. The introduction of NGS has amongst other applications established a new tool for gene expression analysis now termed RNA-seq. The Core Facility supports users with the preparation of NGS libraries for the Illumina technology, sequencing and bioinformatic analysis of gene expression data.

 
Microdissection

Laser Capture Microdissection (LCM):
Tissues, in particular, tumor tissues, are complex structures composed of heterogeneous mixtures of morphologically and functionally distinct cell types.
By allowing the dissection of specific cell populations within a tumor or tissue sample, laser capture micro-dissection facilitates the retrieval of material for RNA, DNA and protein analysis. Frozen tissue or formalin-fixed paraffin-embedded (FFPE) tissues are sectioned on a cryomicrotom. Discrete structures within the tissue are discerned by a quick staining step and light microscopy. Dissected cells are captured onto a sterile plastic surface, which is then transferred to a sample collection tube containing the appropriate cell lysis buffer.

Publications:
Gene expression profile of vascular endothelial growth factor (VEGF) and its receptors in various cell types of the canine lymph node using laser capture microdissection (LCM) 1, Veterinary Immunology and Immunopathology

"BPV-1 infection is not confined to the dermis but also involves the epidermis of equine sarcoids" 2,  Veterinary Microbiology

 

Cell culture

A fully equipped cell culture lab (biosafety level 2) is available to researchers. The team of the Core Facility provides support in the cultivation of cells and execution of experiments.

 
Isolation tubes with beads

Tissue homogenisation:
O
ptimised amounts of ceramic, steel or glass beads prefilled in 2 ml screw-cap tubes are used to homogenise different tissue types on the MagNALyzer (Roche Diagnostics)

 
Qiacube isolation robot

Semiautomated sample processing:
Low throughput sample processing can be performed on the sample processing platform QIAcube (Qiagen). This platform allows to fully automate the processing of almost all Qiagen consumable products. The platform can be used with more than 100 spin column–based protocols for DNA, RNA, and protein sample processing.

 
Lab on the chip

2100 Bioanalyzer/4200 TapeStation:
The Agilent Bioanalyzer and TapeStation are the most frequently used microfluidics-based platforms available, offering solutions for the analysis of DNA, RNA, proteins and cells. Within 30 minutes high quality digital data are delivered. For example, the quality/integrity of RNA can be assessed based on its RNA Integrity Number (RIN)

 
RNA and DNA assay design (general image)

Assay design:
Design of various real-time PCR formats for detection of DNA, mRNA or small RNAs like miRNA etc. Either probe-based formats (molecular beacons, TaqMan probes, TaqMan probes incorporating Locked Nucleic Acid (LNA) monomers, TaqMan minor groove binder probes) or fluorogenic double-stranded DNA-binding dye-based formats can be offered.

 

Head

Reinhard Ertl, MSc
+43 1 25077 3169
e-mail to Reinhard Ertl  




 

Staff

Mag. Melanie Korb
+43 1 25077 3162
email to Melanie Korb

Sarah Schlosser, Dipl. Biol.
+43 1 25077 3169
email to Sarah Schlosser