CF Next Generation Sequencing

The Facility provides next-generation DNA sequencing (NGS) technology to the FLI. External users may also have access to the technology, e.g. upon collaborative arrangements. In addition to sample DNA/RNA quality check, library preparation and sequencing, the facility provides first-pass data processing, data quality check and analysis. A number of pipelines for deeper data analysis are established and available, also via the CF Life Science Computing of the FLI.

Beyond analyzing whole genomes or subfractions thereof (e.g. exomes), NGS is ideally suited to provide insight into fundamental biological processes, such as transcription, translation, DNA methylation, histone modification, protein-nucleic acid interaction and much more.

The Facility operates the following technology platforms:

  • Illumina NovaSeq6000
  • Illumina NextSeq500
  • Illumina MiSeq
  • MinION (Oxford Nanopore)
  • Fluidigm C1 device for single-cell polyA+-RNA/DNA preparation
  • 10x Chromium Controller single-cell preparation.
  • RNA-Seq (full-length transcripts): sequencing of polyA+/rRNA-RNA for analysis of differentially expressed genes or transcriptome assembly
  • RNA-Seq (3'-ends): sequencing of 3'-ends of polyA+ RNA for analysis of differentially expressed genes or identification of transcription termination sites (TTS)
  • CAGE-Seq: sequencing of 5'-ends of polyA+ RNA for identification of transcription start sites (TSS)
  • SmallRNA-Seq: sequencing of small/micro RNAs for expression profiling
  • ISO-Seq: sequencing of polyA+RNA for transcriptome assembly/transcript isoform discovery
  • ChIP-Seq: sequencing of DNA following chromatin immunoprecipitation to identify protein binding sites
  • ATAC-Seq: genome-wide sequencing of transposase accessible DNA (open chromatin)
  • WES: whole exome sequencing for variant discovery
  • WGS: whole genome sequencing for variant discovery or genome assembly
  • Amplicon-Seq: amplicon sequencing for variant discovery or DNA methylation analysis
  • WGBS/RRBS: whole genome/reduced representation bisulfite sequencing for DNA methylation analysis (5mC and/or 5hmC)
  • scRNA-Seq: sequencing of 3' ends of polyA+ RNAs of single cells for analysis of differentially expressed genes
  • scATAC-Seq: genome-wide sequencing of transposase accessible DNA (open chromatin) in single-cell resolution
  • scMultiome: combined scRNA-Seq and scATAC-Seq in single-nuclei resolution

Internal users:
Project Sheet (PS) for requesting NGS

Quality check form (QCF) for requesting QC of RNA/DNA

Knowledge Repository Resources and Cost Calculation

External users:
Please inquire.


Marco Groth+49 3641 656054eMailCore Facility Manager
Martin Bens+49 3641 656801eMailPostdoc
Ivonne Görlich+49 3641 656242/6442eMailTechnical Assistant
Cornelia Luge+49 3641 656242/6442eMailTechnical Assistant
Christoph Englert+49 3641 656042eMailScientific Supervisor

* incomplete due to Data protection

For publications of individual CF members:  publications search 


Marco Groth
CF Manager
+49 3641 65-6054

Christoph Englert
Scientific Supervisor

Group Website

Overview CF DNA Sequencing