GeneCore processes users’ samples with the help of top-end instruments.

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.

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 HiSeq2000, HiSeq4000 and cBot instruments, as well as MiSeq and NextSeq sequencers. 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, AAT Fragment Analyzer, Qubit, and more). To deal with increasing numbers of incoming samples, we recently reinforced our instrumentation infrastructure through acquisition of Beckman FX liquid handling robots.

Major projects and accomplishments

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

  • 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).

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 around 100 terabases of MPS sequence data for its users. GeneCore staff also train individual researchers and organise practical courses on corresponding subjects.

Services provided

  • MPS sequencing, microarrays (homemade, commercial).
  • miRNA qPCR profiling, Bioanalyzer, liquid handling robotics.
  • Access to instruments and complete support: qPCR, NanoDrop, PCR cyclers.

We offer processing of samples for a range of microarray applications (mRNA, miRNA and other ncRNA expression profiling, comparative genome hybridisation) available from Affymetrix and Agilent platforms and, upon demand, spotting of customised arrays. In addition to three qPCR instruments managed by GeneCore, our qPCR capacity has been considerably enhanced by a Fluidigm Biomark HD instrument – a device capable of quantitation of transcripts on a single cell level.

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, NuGEN and Beckman Coulter. During 2014 we began an extensive collaboration with New England Biolabs and Hamilton aiming at implementation of NEB MPS protocols to automated liquid handling robots.

A detailed overview of the GeneCore activities can be found at