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In May 2013 I joined a pilot project aiming at establishing a single cell platform, SiCell, as part of SciLifeLab headed by Prof Stefan Bertilsson at Limnology/EBC and Thijs Ettema at Molecular Evolution/BMC. As the machine park and lab facilities are located at BMC, I have the opportunity to share office space with the skilled biologists and bioinformaticians in the Ettema lab – what a great gang!
Together with my colleague Claudia, I am setting up an infrastructure for single cell analysis with focus on microbial genomics that will enable researchers in the scientific community with an interest of single cell analysis to perform their analysis. The applications range from studies of genetic diversity, evolution to medicine and allow identification of the vast majority of uncultured microorganisms.
One of the biggest challenges when working with small amounts of DNA or RNA, is to work very clean to limit the risk that contamination obscures your real results. This is done by adhering to strict laboratory practice but also by minimizing the human handling of samples using robotics in closed clean environments. Moreover, the results obtained are especially sensitive for random artefacts that have to be considered during subsequent data analysis. To be able to analyse single cells, we use advanced FACS (fluorescence activated cell sorting), cell lysis and whole genome amplification followed by library construction and next generation sequencing.
During my PhD studies at Rudbeck Laboratory in Prof Marie Allen’s group, I worked mainly with method development and optimization of technologies such as microarrays and pyrosequencing to be able to analyse forensic material in scarce amounts of poor quality. This kind of analysis has similarities with single cell analysis as it shares, more or less, the same challenges of avoiding contamination and working with a starting material that often is far from optimal. Before joining SiCell, I had the opportunity to plunge in to the fascinating world of parasites during my years at The National Veterinary Institute. There I gained useful experience in cell biology doing, amongst other things, cell culturing and cell cycle analysis using flow cytometry of Giardia lamblia.