/Enhanced messenger RNA localization for spatial transcriptomics using precision-engineered substrates

Enhanced messenger RNA localization for spatial transcriptomics using precision-engineered substrates

PhD - Leuven | More than two weeks ago

Microfabricate your path to improve medical insights into the transcriptome
Spatial transcriptomics is a method for analyzing gene expression by identifying and quantifying mRNA in tissue slices with cellular or sub-cellular spatial resolution.  The method produces data-rich information that yields insights into the heterogeneity of cell types within a tissue section as well as elucidate the individual functioning of the cells.  Applications include oncology (the diagnosis and treatment of cancer) and immunology (functioning of the immune system), among others.

Different methods of mRNA extraction from tissue samples exist but one technique is to fixate the tissue sample onto a glass slide and transfer the mRNA contained within the sample through a buffer solution onto the surface of the slide.  Once immobilized on the glass slide, the mRNA can be analyzed using techniques such as single-molecule fluorescence in situ hybridization (smFISH).  A key challenge is the process of transferring the mRNA from the tissue to the slide while maintaining spatial information since diffusion will de-localize the mRNA from the host cells.  The focus of this topic is to leverage the microfabrication capabilities of imec to produce precision-engineered substrates for improved localization and capture of the mRNA.

The role of the selected student will be to design, develop and experimentally validate a microfabricated device for improved mRNA localization and capture relevant to spatial transcriptomics. Diverse physical mechanics employing microfluidics, electrostatics or electrokinetics, acoustics and photonics for better localization while counteracting diffusion will be considered. The student will make extensive use of computational tools to aid in the study.

Prospective candidates should have strong analytical skills and preferably, prior knowledge in applying numerical methods to fields such as fluid mechanics, solid-state physics, electrochemistry and/or electrophysiology. At imec, the selected candidate will work in a dynamic, multi-disciplinary team and gain expertise in the development of microfabricated devices for life science applications.

Required background: Engineering Science or Physics

Type of work: 50% modeling and numerical simulations, 40% experiments, 10% literature review and publication-related activities

Supervisor: Liesbet Lagae

Daily advisor: Ben Jones

The reference code for this position is 2024-130. Mention this reference code on your application form.

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