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.

Major projects and accomplishments

GeneCore provides its services to a broad range of users ranging from small research groups to large consortia (the International Cancer Genome Consortium, for example). The implementation of new-generation sequencing technology was a vital step to ensure EMBL remains at the forefront of European research. Since 2010, our massively parallel sequencing (MPS) suite has been upgraded and expanded significantly and now includes HiSeq2000 and cBot instruments, as well as MiSeq and Ion Torrent sequencers. 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.

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 (including strand-specific libraries).
  • 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.

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 and freely accessible tools. To date, GeneCore has generated around 100 terabases of MPS sequence data for its users.

Training is another crucial aspect of our work – GeneCore staff tutor individual researchers and also 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 is still 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.

A detailed overview of the GeneCore activities can be found at