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The NGS core facility is running two different NGS technologies, each of which have advantages/disadvantages depending on the application. Specifically, four different NGS platforms including the Illumina NovaSeq6000, Illumina NextSeq550 as well as an IonTorrent PGM System are being used. In order to allow single cell sequencing, the lab runs a 10x Genomics platform that uses droplet technology to generate single cell suspensions. All platforms are run as operator-based systems.
Illumina NovaSeq6000
The NovaSeq6000 system performs large-scale sequencing efficiently and cost-effectively. Its tunable output generates up to 6 Tb and 20 B single reads in dual flow cell mode with streamlined workflows. The system offers sequencing of up to 48 genomes, 500 exomes or 400 transcriptomes in ~2 days in a single run with comprehensive coverage.
Features
Data Generation
Instrumentation
Illumina NextSeq 550
The Illumina NextSeq® 550 is the largest desktop next-generation sequencing (NGS) system from Illumina capable of sequencing a 30x human genome in a single run. Two different flow cell options and multiple reagent configurations are providing a maximum application flexibility (130 to 400M clusters; 40 to 120 Gb).
Accordingly, the system is suitable for a high number of different applications, e.g. whole exome- or genome sequencing, RNAseq, targeted resequencing or gene expression profiling and single-cell sequencing. The sequencing technology is based surface-based bridge amplification for clonal amplification and sequencing of each generated cluster using the Illumina "sequencing by synthesis" (SBS) method with reversible terminator chemistry.
Ion Torrent PGM
The DNA-Sequencing on the desktop NGS system PGM from Ion Torrent Life Technologies is based on the principle of Semiconductor Sequencing developed in 2007. This technology allows a real-time measurement of hydrogen ions produced during DNA replication and thereby directly translates genetic information (DNA) to digital information (DNA sequence).
This is enabled by an ion semiconductor chip on which the sequencing reaction takes place. The different available chips allow a flexible output for ultimate project flexibility. Additonally, the sequencing times are short, e.g. 30 min for a 1 x 35 bp on a 314 chip or 8 hours for a 1 x 400 bp run on a 318 chip.
10x Genomics Chromium iX
The Chromium iX allows for high-throughput single cell transcriptome, immunome, multiome or cell surface protein analyses in a variety of cell types as wells as nuclei from fresh or fixed samples (including FFPE). The flexible workflow encapsulates single cells or nuclei together with gel beads intro nanodroplets. The underlying GEMCode Technology enables the execution of thousands of micro-reactions in parallel. A GEM is a „GelBead in EMulsion“ droplet that encapsulates each micro-reaction within the Chromium System. 10x Genomics offers a multitude of kit solutions including gene expression, chromatin accessibility, cell surface proteins, immune clonotype, antigen specificity, and CRISPR perturbation screens.
Other Instruments
Library preparation & preparation for sequencing
Quality control: Agilent 2100 BioAnalyzer, Agilent TapeStation 4150
Fluorometer: Invitrogen Qubit 4
Spectrophotometer: NanoDrop 1000
