Consultations
The Next Generation Sequencing Core offers support for your Sequencing project from initial idea, selecting an optimal design, identifying the best-fit sequencing approach, and assisting in proposal writing. This applies whether you are choosing to sequence with us or prefer an ordinary of-the-shelf solution provided by commercial sequencing providers, in which case we can also help you navigate the various terminologies.
Implementation
We are happy to advise on nucleotide purification methods, perform quality controls, generate libraries, and finally handle the generation of sequencing data for your project.
Applications
We can help you with almost any NGS application for your project.
For this purpose we offer in-house library preparation and sequencing for small or difficult projects.
For completely commercially standardized applications we also help you find the the best deal at a reliable commercial partner.
The applications most frequently performed at the core are:
- 3′-mRNA seq for direct gene expression analysis
- including sequencing of low-input or very degraded RNA, eg. FFPE-derived RNA, for which we have developed un-rivalled optimized methodology
- mtRNA-seq, with and optimized in-house protocol
- Custom-barcode seq for projects where the barcodes are the readout
- Cancer-hot-spot gDNA seq
- Single-cell RNA seq
Custom designs
We have a decade of experience in adapting the tools of library generation to generate new protocols to fit special project needs. Especially for novel RNA-seq approaches (examples: mt-tRNA seq, very-low input expression profiling, total small-RNA seq (20-200nt), and expression profiling of very degraded FFPE-derived RNA) In addition to enabling successful project completions, this has led to the Core attaining designation of “ION-Torrent RNA-seq reference lab” and the winning of the international Lexogen Research Award.
Data delivery and Analysis
We deliver filtered quality data, either in fastq or ubam format for downstream analysis. For certain applications we can additionally offer mapping to a reference genome.
We collaborate closely with the HPC/Bioinformatics facility, hosted by the Institute for Bioinformatics, and recommend that you contact them for assistance with data analysis.
For contact details please see >> Contact.
Teaching
As an integral part of the Medical University Biocenter, we offer several courses in NGS project design, library generation, sequencing, and data analysis.
