Genomics Core Facility

GeneCore is the in-house genomics service centre at EMBL

GeneCore is the in-house genomics service centre at EMBL equipped with state-of-the-art technologies required for functional genomics analyses and operated by highly-qualified staff. 


What we do

The Genomics Core Facility (GeneCore) provides its services to a broad range of users ranging from small research groups to international consortia.

Our massively parallel sequencing (MPS) suite boasts Illumina sequencers – NextSeq500, NextSeq2000, and MiSeq as well as PacBio Sequel IIe. We also work in close collaboration with the University of Heidelberg and the German Cancer Research Center (DKFZ) to further enhance the capabilities of these sequencing technologies.

Preparation of MPS libraries for various applications is supported by a robust instrumentation infrastructure (e.g. Covaris, Bioanalyzer, Agilent Fragment Analyzer, Agilent Femto Pulse, Qubit, and more).

To support processing of large quantities of samples we have employed a suite of liquid handling robots such as the Beckman Coulter i7, FXp, Echo acoustic liquid handler, and Dispendix iDot.


GeneCore website maintenance

Due to unforeseen circumstances the GeneCore website is currently undergoing major maintenance. Please contact us at solexa@embl.de if you would like to submit samples for sequencing. We are sorry for any inconvenience this causes. In the meantime, please use the form that you can download below.

Major projects and accomplishments

GeneCore provides the following analyses in a single-end or a pair-end sequencing mode, including multiplexing:

  • Genome-wide location analysis of nucleic acid-protein interactions – ChIP-Seq, CLIP-Seq.
  • Transcriptome sequencing: RNA-Seq.
  • Discovery of small non-coding RNAs: ncRNA-Seq.
  • Genome-wide DNA methylation analysis: Methyl/BS-Seq.
  • De novo sequencing & re-sequencing of genomic DNA.
  • Targeted enrichment (sequence capture) in solution coupled with MPS.
  • Single-cell genomic applications (scRNA-Seq, scDNA-Seq).
  • And much more.

GeneCore continues to establish new protocols enabling the processing of challenging samples such as low input or metagenomics samples.

For analysis of MPS data, we work intensively with EMBL’s bioinformatics community on the development of in-house, freely accessible tools.

To date, GeneCore has generated more than 100 terabases of MPS sequence data for its users. GeneCore staff also train individual researchers and organize practical courses on corresponding subjects.

Services provided

  • MPS sequencing.
  • miRNA qPCR profiling, Bioanalyzer, liquid handling robotics.
  • Access to instruments and complete support: qPCR, NanoDrop, qbit, Agilent Bioanalyzer, and PCR cyclers.
  • Consultation and experiment design advice.

Technology Partners

MPS continues to be a very dynamic and rapidly evolving technology. We collaborate with several companies involved in developing MPS-related products, for instance testing them in our workflows. GeneCore is a member of the early-access program of Illumina, Agilent, NEB, Dispendix, and Beckman Coulter.

A detailed overview of the GeneCore activities can be found at www.genecore.embl.de.


Genomics Core Facility
EMBL Heidelberg,
Meyerhofstraße 1,
69117 Heidelberg,

Tel:+49 6221 387- 8486/ -8492
E-mail: genecore@embl.de