ESR 6 – Development of methodology for single cell organism genome analysis


  • Research project

    Much improvement and technical quality checks are still needed to reach the full potential of SCG for microbial eukaryotes, especially along critical steps of high-throughput sequencing and preliminary bioinformatic analysis. Indeed, eukaryotes have much more complex genomes than prokaryotes, and optimal solutions for all these steps are fundamental to obtain meaningful genome assemblies that can be readily exploited for addressing unsolved scientific questions. The main objective of this ESR is the establishment of methodology for single cell whole organism genome characterization. This will consist of implementing the best laboratory procedures for single cell handling, isolation by Fluorescence Activated Cell sorting directly into microtitre plates, lysis procedures, improving DNA accessibility, DNA amplification, RNA handling, library preparation, process automation, sequencing, process quality control, and data analysis procedures for do novo assembly of the obtained genomes. All these steps still need fine refining, and all of them are fundamental for a good success of the methods and science proposed in SINGEK.

  • Supervisor


    Ivo Gut


  • PhD Program

    Biomedicine, Universitat Pompeu Fabra

  • Expected Results

    Procedures and data analysis methodology for single cell studies of species for which no reference genome sequences exist. Methodology establishment of homogeneous DNA amplification from single cells, de novo genome assembly, RNA analysis, de novo transcriptome assembly.