Next generation sequencing, also sometimes called deep sequencing, is our core business. We have a team of over 10 people, both wet lab technicians and bioinformaticians, to support the research and the clinical application of this technology using multiple Illumina HiSeq2000 and MiSeq machines.
The applications for this technology are widespread, still growing and are common practice in the institute. Every aspect of the deep sequencing process is supported by the GCF that, as a facility, has a large body of experience and knowledge. The facility has been using Illumina technology from the early onset of the NGS development in 2009 and therefore we are now in a position to support the users with clear advice as to how the experiment should be designed to increase the success rate of the experiment. We are open to suggestions and are flexible in the way users want to have their samples analyzed with regard to sequence depth and numbers of libraries that are pooled in multiplexed experiments.
The facility is set up according to a fee-for-service model where the material and chemistry cost prize is the main factor that determines the fee, this makes our support very affordable compared to external service providers.
Facility users can provide cells or tissues as starting material but we also work with purified RNA or DNA as well as ready to sequence DNA libraries. All the necessary equipment for the preparation of sequence libraries and the associated quality control steps are in house. For some applications, like RNAseq, the demand is so high that we run the sample preparation in 96-wells format using PE SciClone robotic pipetting systems.
The bulk of the experiments are performed using validated Illumina protocols and kits, but extensive experience has made it possible to either adapt, or develop new protocols for creating sequencing libraries. This is often done in close collaboration with the end user. New developments are closely followed and can be implemented relatively quickly.
The data generated by the sequencing machines is stored on a central server system and analyzed by the facilities bioinformaticians. All data can also be made directly available to the user in the desired format. We have pipelines for demultiplexing the data, the alignment of the reads to genomes of choice and experiment specific downstream analysis. We can provide the results in tabular or graphical formats or prepare them for visualization in genome viewers like IGV (http://www.broad.mit.edu/igv/). We also host licenses for third party software solutions for analysis like Ingenuity and Nexus.
HiSeq2000 (2x), MiSeq, cBot, Perkin Elmer NGSx Sciclone Workstation, Covaris, Agilent BioAnalyzer, Perkin Elmer-Gx system, Biomek Fx, Agilent Scanner, Illumina Beadarray Reader, Tecan Hybstations, Nimblegen Hybstation, MicroGrid Printrobot.