Deutsch Intern
    Core Unit Systems Medicine


    NGS solutions

    The Core Unit provides access to Next Generation Sequencing (NGS) technologies for molecular high-throughput investigations of RNA and DNA:

    • RNA-Sequencing (RNA-Seq for Gene Expression- and Trancriptome Analysis)
      • mRNA-Sequencing with Oligo-dT-capture beads (Eukaryotes)
      • total RNA-Sequencing with Random Primer
      • total RNA-Sequencing after Depletion of Globin-mRNA or rRNA (Prokaryotes and Eukaryotes)
      • small RNA-Sequencing, i.a. for bacterial transcriptomes
      • Dual-RNA-Sequencing of Prokaryote- and Eukaryote-RNA (human, mouse)
    • Single Cell-RNA-Sequencing (scRNA-Seq)
      • 10x Genomics Droplet Microfluidics (up to 10.000 cells)
      • FACS-sorted single cells analysis according to the SMART-Seq v4 Ultra Low Input protocol (1-300 cells)
    • Whole-Genome-Sequencing (WGS), i.a. bacterial and viral genomes

    • Whole-Exom-Sequencing (WES)

    • Amplicon-Seq (targeted sequencing of PCR-Amplicons, e.g. with Phase-Shift-Primer)
      • PCR amplification & metagenomic DNA-sequencing of the 16S rRNA gene for the classification of the microbiome
      • PCR amplification & mRNA-sequencing for the analysis of the immune repertoire: IgG / IgM, as well as B-cell and T-cell receptors (human / mouse)
    • Sequencing of methylated DNA (Methyl-Seq)

    • ATAC-Seq (chromatin accessiblity) 

    • ChIP-Sequencing (ChIP-Seq – analysis of protein interactions with DNA)

    • RIP-Sequencing (RIP-Seq – analysis of protein interactions with RNA)

    • CLIP-Sequencing (CLIP-Seq – analysis of protein interactions with RNA-binding motives after UV-cross-lining)

    • Customized molecular biology solutions on request as a collaborative project


    The Core Unit offers customized analysis solutions for NGS projects at various levels:

    • Bioinformatics consultation

    • Standardized data analysis workflows for various NGS applications:
      • Gene expression analysis
      • Functional enrichment and signalling pathway analysis
      • Identification of protein binding sites (peak calling)
      • ...
    • Development of analysis pipelines for new applications on request

    • Support in the transfer of NGS experiments for publication on SRA (Sequence Read Archive) and GEO (Gene Expression Omnibus)