The Illumina NextSeq 1000 offers diverse applications for high-throughput DNA and RNA-sequencing.

Further information can be found on the Core Facility Imaging (CFI) website.


  • Transcriptome analysis using RNA-seq (mRNA, lncRNA, medium-sized RNA, smallRNA)
  • Translation control using Ribo-seq
  • Binding analyzes using ChIP- and CLIP-seq
  • Genome analysis using Whole Genome-seq or Exom-seq
  • Oxford Nanopore DNA/RNA-seq data
  • Quality control of raw data
  • Removal of adapter sequences and quality trimming
  • Mapping (assignment of reads to known reference genomes)
  • Annotation (assignment of mapped reads to known genes)
  • Determination of read coverage
  • Normalization (regarding RNA composition, transcript length, differential expression etc.)
  • Determination of differentially expressed genes
  • Correlation of mRNA to miRNA expression (incl. target analysis)
  • Determination of the expression of alternative isoforms (e.g. due to alternative splicing)
  • Quantification of translation efficiency (Ribo-seq)
  • Analysis of binding profiles (ChIP- and CLIP-seq)
  • Determination of effector pathways using gene annotation enrichment analysis (GAEA) and gene set enrichment analysis (GSEA)
  • Metagene analyses, inclusion of "public data" (e.g. TCGA) and further analyzes on request
  • Support for Oxford Nanopore sequencing
  • Optional library preparation (barcoded)
  • data analysis

List of fees for the evaluation and further analysis of NGS data on known genomes.


Service Medical Faculty MLU (not Med. Faculty) Billing Unit (BU)
Consultation 30€ 50€ per call
Quality control small RNA (RIN) 55€ 70€ per chip (max. 11 samples/chip)
Quality control RNA (RIN) 40€ 50€ per chip (11-12 samples/chip)
Primary Analysis 10€ 20€ per 20 million reads¹
Secundary Analysis 25€ 30€ per analysis


 ¹ Per started billing unit.

Data retention for 3 months.