The laboratory allows high throughput annotation and functional analysis of alternative splicing (AS) in humans. Using cancer-related genes as targets, the Centre has undertaken a systematic investigation of splice isoforms. The study comprises high throughput, tissue specific AS annotation and functional characterization of alternative isoforms following specific inhibition using siRNA or antisense techniques for the reprogramming of splicing. This work aims to elucidate the mechanism of cancer related AS, and will lead to the identification and characterization of validated novel anti-cancer targets suitable for diagnostic and drug discovery applications.

Experiment design and data storage

A series of components were developed for the design and management of different types of experiments, mostly done in high-throughput with microplates and robots. The software currently supports the design of microplates for multiple purposes like transfection, viability assays, oligo storage, caspase assay, RT-PCR, Real time PCR, etc. The microplate design module is highly dynamic and uses a spreadsheet web interface similar to Microsoft Excel. The designed experiments are transfered to the robots and generated results are then automatically re-imported into the LIMS.

Products management

The LIMS is also responsible for the ordering and management of all laboratory products. Oligos, antibody and other types of products are stored, linked to experiment design and used in the analysis of the results. Information concerning these products can be quickly retrieved using the barcode search.

Analysis

Many tools were developed to interpret and visualize experiments results in various ways. These graphic tools help the scientist to quickly identify failed experiments and results that need to be investigated further. Results are displayed in a gene centered view along with other publicly available information concerning the genes themselves like isoforms annotation from different sources (EnsEMBL, NCBI, AceView), alternative splicing events, predicted protein domains, position of ordered oligos, etc.