ESR 10 Raphaelle Lesage works at KULeuven and she recently did a secondment at UKK in Cologne. Here below she tells us about this experience, inside and ouside the lab.
The purpose of this short secondment was to report my advances and get feedbacks on the (pre)processing of microarray data for the purpose of integration into the in silico model. Indeed,automatic inference of a gene regulatory network requires an informative dataset. Ideally, it would consist of a large set of gene-expression profile data representative of perturbations of the cellular systems under study. However, in complex systems such as human or mouse cells, such systematic experimental perturbation approach is challenging. It was reported that similar dynamic richness can be efficiently achieved by assembling a considerable number of naturally occurring and experimentally generated phenotypic variations of a given cell type. In order to gather enough perturbation data, a pipeline for cross-platform integration was developed. It enables to merge and remove batch effect from various gene expression datasets relative to mouse cartilage in osteoarthritis.
During the secondment, integration of an additional dataset from a different platform (Agilent) was investigated with the support of Prof. Dr. Bent Brachvogel, in addition to the technical discussions about the pipeline. I also got an introduction to a data processing software (GeneSpring®) and the opportunity to work on the provided dataset with this software. In parallel, I got interesting talks with ESR4 (Mengji Zhu) and feedbacks from a biology and biochemistry perspective. Finally, I have been very well welcomed by all the lab’s members. It was particularly interesting to be in immersion in a different environment, to discover the habits and the way of working of another lab.
Thanks to the warm welcome of Mengji, I also discovered the lovely city of Cologne and its beautiful cathedral. I learnt that, when springtime comes, German people start being crazy about the ‘Spargel’ (asparagus). We couldn’t help but trying them, but, never without the famous Kölsch beer of course! Many thanks to CarBon for giving me this great opportunity to travel, exchange and work with other researchers all over the Europe.