Genomics Core Facility
EMBL's Genomics Core Facility is equipped with state-of-the-art hardware required for transcriptome and global location analyses and is operated by highly-qualified staff. As training is an inseparable part of GeneCore activities, its staff is involved in tutoring individual researchers as well as in organising practical courses on subjects such as quantitative real-time RT-PCR (qPCR) or gene expression profiling and its data analysis.
Major projects and accomplishments
MicroRNAs (miRNAs), a group of small non-coding RNA molecules, are now recognised as an important regulator of gene expression. Their characterisation, together with attempts to elucidate mechanisms of their action, is currently one of the hottest and most challenging areas in molecular biology. Detailed analysis of miRNAs is technically demanding because their mature form is only ~22 frequently highly homologous nucleotides long. In partnership with Matthias Hentze's group (page 52) GeneCore has worked on the development of the locked-nucleic- acids based oligonucleotide array miChip. This system, whose performance is further refined, enables profiling of mature microRNAs from human, mouse and other organisms. This valuable platform is complemented with a complete panel of qPCR TaqMan miRNA assays for human, mouse and Drosophila.
In 2007 the DNA sequencing service team processed 43,000 reactions on samples from almost all wet lab groups from Heidelberg and Grenoble and some from Hamburg. Two 96-capillary sequencers MegaBACE are currently employed, and sample, data and work flows are fully supported by the electronic sample registration and tracking system we have developed and implemented.
During 2007 the DNA microarray team also dealt with increased number of samples submitted for genome-wide studies of DNA sequences bound by regulatory or modifying proteins, so called location analysis, on high-density tiling arrays (ChIP-on-chip).
Services provided
In principle,the activities of GeneCore are divided into three modes of operation:
- project-focused: microarrays (home-made, commercial), liquid handling robotics for medium-throughput pipetting projects and SAGE (Serial Analysis of Gene Expression);
- sample-focused: DNA sequencing, Bioanalyzer; miRNA qPCR profiling;
- access to instruments and complete support: qPCR, NanoDrop, PCR cyclers, microarrayscanner, high-capacity vacuum concentrator
GeneCore offers sample processing on four different platforms from Affymetrix. In addition to traditional '3'-end' arrays, exon arrays enable the study of alternative splicing patterns of individual transcripts at an unprecedented depth. In 2007 we implemented gene arrays, a new format launched by Affymetrix recently for analysis of whole-transcript expression; and tiling arrays are used for annotation-independent transcriptome profiling. In 2007, GeneCore processed around 1,600 samples in total. Acquisition of a highly sensitive Agilent scanner further enhanced the facility's capacity to process spotted microarrays.
Three qPCR instruments managed by GeneCore are primarily used for gene transcript quantification to corroborate microarray results as well as for detailed DNA occupancy profiling after chromatin immunoprecipitations. With our assistance, EMBL researchers analysed about 150,000 qPCR assayed points in 2007.
The acquisition of new-generation sequencing technology is vital to keep EMBL at the forefront of European research. In 2007 the decision was made to purchase the Genome Analyzer (Solexa) by Illumina. This system will become operational during the first quarter 2008 and will be used for deep sequencing analyses of occupancy profiles and non-coding RNAs.
A detailed overview of the GeneCore activities can be found at www.genecore.embl.de.