Christen Lab, Genomics, Quantitative Transposon Sequencing

Background

In the Christen lab we are using hyper-saturated transposon mutagenesis coupled to high-throughput sequencing to study the cellular core networks fundamental for life. Using this technology, we decoded the essential genome of a bacterium with near base pair resolution (Christen et al. MSB, 2011). The current analysis pipeline uses a binary classification scheme to discriminate essential DNA sequences from non-essential ones. Our group now develops quantitative transposon sequencing approaches ( qTnSeq ) that will enable us to profile the fitness landscape of genomes with unprecedented accuracy. This technology will open up new avenues to map and reconstruct global genetic interaction networks.

Project

The goal of this master project is to develop a quantitative TnSeq strategy that will enable us to map fitness costs of insertion perturbations across an entire bacterial genome. This technology will be based on a novel PCR-barcoding strategy to tag amplification product prior high-throughput DNA sequencing. A hyper-saturated transposon library will be constructed and subjected to serial outgrowth. Detailed bioinformatic analysis will be performed to calculate insertion site frequencies and quantify fitness effects of individual transposon perturbations.

Skills: Interest in Systems-genetics, multiplexing technologies and high-throughput DNA sequencing analysis.

Duration: 3-6 months, position immediately available

Supervision and more information: Beat Christen