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.
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.
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.
Tissue homogenisation Optimised 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)
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)
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.
Single cell analysis The 10x Genomics Chromium system is a scalable microfluidics-based solution for comprehensive single cell gene expression profiling and cell characterization.