Genomics Core Facility

GeneCore is the in-house genomics service centre at EMBL

Rules of access

A. Operational Settings

  1. All users need to be registered in the GeneCore database under a specific principal group. This group is assigned by GeneCore only upon request (please contact us at benes@embl.de). We require the following personal and professional details: name, business address, incl. phone number and email address; this information is used to prepare a principal user group and user accounts in the GeneCore registration system, and thereafter stored for a period of interaction with GeneCore.
  2. All samples need to be registered in the GeneCore sample submission system before their shipment to GeneCore. You are expected to provide us with all relevant information relating to the samples, together with full details of any known hazards relating to them. For shipment to EMBL, please note the following additional instructions: samples are clearly labeled and packed in a bag or in a sample box (no loose tubes please).
  3. Samples are primarily processed in sequential order (first come first serve). GeneCore staff may, if necessary and in rare circumstances, change the order of samples (for instance, to fully use available sequencing capacity), or even reject processing of samples completely.
  4. Sequencing results are delivered to the user electronically in FASTQ format (and optionally alignments in BAM format) via IBM Aspera technology (fasp2 transfer protocol).
  5. Data are available for download for a maximum of 4 weeks. Afterwards data is deleted at GeneCore.  Data are archived for 10 years but users are fully responsible for proper management and long-term storage of their data.
  6. GeneCore Bioinformatics staff is primarily responsible for the sequencing data production and quality control. Further Bioinformatics data analysis consulting and support is only possible upon request and ideally requested prior to sample submission.

B. Sample Settings

  1. NGS projects require DNA or RNA as input for GeneCore to prepare sequencing libraries. Finished, ‘ready-to-run’ libraries are also accepted; however, in this case GeneCore is not responsible for any issues related to library preparation.
  2. All samples have to meet quality & quantity criteria available on the GeneCore webpage or communicated to the users by GeneCore staff.
  3. Users are responsible to fulfill all legal, ethical and regulatory standards associated with the sequenced samples and ensure proper anonymization of sample identifiers, and by providing the samples to EMBL for sequencing, they are confirming to EMBL that all relevant consents, licenses, or approvals have been obtained and applicable standards been complied with.
  4. Unless requested otherwise by the user, samples will be disposed of after six month or returned at cost of the user within 30 days after the sequenced data has been released.
  1. Sequencing data obtained from samples provided to EMBL may only be used for academic and scientific purposes, but under no circumstances for any non-civilian purposes, or purposes incompatible with basic molecular-biological research.
  2. Users are responsible for data analysis and interpretation.
  3. Although EMBL will use reasonable endeavors to carry out sequencing in accordance with good scientific practice, we do not undertake that data provided by us will lead to any particular result, nor do we guarantee a successful outcome of users’ project. Consequently, EMBL disclaims any liability regarding quality, reliability, reproducibility, fitness for any particular or intended purpose, or otherwise.
  4. Users are required to contribute financially to costs incurred by EMBL, typically based upon number of samples processed, method applied for their processing and the selected instrument and mode of sequencing.
  5. External users from academia, primarily in EMBL member states, can use the sequencing service provided by GeneCore (capacity permitting). They are advised to discuss projects’ conditions & deliverables prior to sample submission.
  6. GeneCore does not claim any ownership of samples or data, both belong solely to the user.
    Anonymized and non-traceable data may be used for statistical and quality control purposes.
  7. All GeneCore contributions to projects have to be adequately acknowledged.
  8. Please contact us at genecore@embl.de in case you need any additional information on sample processing, sequencing or data processing.