Genomics Core Facility
Massively parallel sequencing suite
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. Training is a crucial aspect of our work and staff tutor individual researchers and organise practical courses on complementary subjects.
Major projects and accomplishments
The acquisition of new-generation sequencing technology was a vital step in ensuring EMBL remains at the forefront of European research. Since 2010, our massively parallel sequencing (MPS) suite has expanded considerably and now consists of the Illumina HiSeq2000, cBot and three GAIIx instruments. Preparation of MPS libraries is facilitated by a robust framework of other instruments (e.g. Covaris, Bioanalyzer, Qubit). GeneCore provides the following analyses in a single-read or a paired-end sequencing mode, including multiplexing and mate-pair libraries:
- Genome-wide location analysis of nucleic acids-protein interactions – ChIP-Seq, CLIP-Seq;
- transcriptome sequencing: RNA-Seq;
- discovery of small non-coding RNAs: ncRNA-Seq;
- genome-wide DNA methylation analysis: Methyl-Seq;
- de novo sequencing and resequencing of genomic DNA;
- targeted enrichment (sequence capture) on arrays or 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 provide access to Genome Analyzer and Mining Station by Genomatix and work intensively with EMBL’s bioinformatics community on the development of in-house tools. To date, GeneCore has generated more than one terabase of MPS data for its users.
Services provided
- MPS sequencing, microarrays (home-made, commercial).
- miRNA qPCR profi ling, Bioanalyzer, liquid handling robotics.
- Access to instruments and complete support: qPCR, NanoDrop, PCR cyclers, microarray spotters and scanners, high-capacity vacuum concentrator.
We offer processing of samples for a range of applications (mRNA, miRNA and other ncRNA expression profiling, comparative genome hybridisation, occupancy profiling) suitable for hybridisation to various microarray formats including Affymetrix and Agilent and customised arrays upon demand. Three qPCR instruments managed by GeneCore are primarily used for gene transcript quantification to corroborate microarray results as well as detailed DNA occupancy profiling after chromatin immunoprecipitations or microRNA expression profiling. This valuable platform is complemented by an opened miQPCR system, co-invented with Mirco Castoldi (MMPU. With our assistance EMBL researchers analysed around 150 000 qPCR assayed points in 2010. We also implemented a new application, known as high-resolution melting analysis, which enables the determination of sample homogeneity and the analysis of proteins.
Technology Partners
MPS is still a very dynamic and rapidly evolving technology. Various companies develop new products that need to be tested in our workflows.
A detailed overview of the GeneCore activities can be found at www.genecore.embl.de.