Description of Research Expertise

The Functional Genomics Core offers fee-for-service microarray experimental design, sample hybridization and analysis. The global aim of the Core is to provide our clients with the complete genomic analysis package, from the initial steps of experimental design to the final steps of result interpretation and publication. This unique and comprehensive approach has not only resulted in our consistent production of very high quality data, but has aided our clients in the interpretation of their results and has expedited the process by which their data becomes published. The service we provide can be broken down into these main areas:

• Consultation on experimental design, sample preparation and quality control. Our aim is to work with all investigators prior to their providing samples, so that they can be trained in microarray experimental design and appropriate techniques for sample preparation. We have found that our involvement during the early stages of experimental design results in higher quality end results and avoidance numerous pitfalls.

• Production of high quality microarrays. The Core manufactures and prints in house high density microarrays from human and mouse cDNAs, and tiling arrays for ChIP-on-Chip analysis, using stringent QA and QC measures. All array print runs are rigorously quality controlled by test hybridization to our standard probes. We also work with investigators to print custom arrays based upon the individual project requirements.

• Probe preparation and sample hybridization. The Core has developed highly sensitive methods for sample labeling, detection and microarray analysis. We can produce excellent data sets with as little as 5-25 ng total RNA, or the amount obtained from a single pancreatic islets. We offer a full range of hybridization services including assessment of sample quality, linear RNA amplification, sample labeling and hybridization, batch slide scanning, image quantification, data and pathway analysis. High throughput methods allow for the labeling and hybridization of up to 48 samples in a single day.

• Next generation sequencing. Using a massively parallel sequencing approach, the Illumina Genome Analyzer can generate more than one billion bases of data in a single run. The system leverages Solexa sequencing technology and novel reversible terminator chemistry, optimized to achieve unprecedented levels of cost effectiveness and throughput. Current applications include Whole-Genome Chromatin IP Sequencing (ChIP-Seq), Digital Expression Profiling and Small RNA discovery and quantification.

• Analysis of data and interpretation of results. We have developed significant technical expertise in the area of microarray analysis, and provide data analysis and bioinformatics support as needed. Through the development of in-house scripts using the R language and environment for statistical computing we perform all steps of array analysis, including image analysis and post-processing, normalization and complete statistical analysis. Assistance and advice is also provided with regard to data interpretation, pathway analysis and strategies for publication.