Imaging of Human Pluripotent Stem Cells for Spatial Patterns of Gene Expression

FUNDING: 10 weeks (full time, 37 hrs per week, £12 per hour, £850 consumables, £500 student accommodation bursary)
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LOCATION: Sheffield, UK

Dr Samantha Ivings, Biology, Sheffield

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Human pluripotent stem cells (hPSCs) offer an excellent model for understanding how coordinated gene expression impacts the spatial organisation of cells during development, in vitro. In this project the student will use a programming software of their choice (such as R, MATLAB, Python) to analyse time-lapse videos of hPSCs being differentiated to hypothalamic progenitors. The cells have been engineered to express the fluorescent protein GFP as a marker of the SIX6 gene, which is involved in hypothalamus development. The student will track the cells, either manually or computationally, then analyse the spatial properties of SIX6. These properties may include SIX6 heterogeneity, heritability (i.e. whether daughter cells have SIX6 expression similar to the parent cell), and relating SIX6 expression to that of neighbouring cells. Ideally, the student will also computationally analyse the trajectory of single cells. This would enable greater understanding of when cells spatially organise in relation to SIX6 expression levels. The goal of this research is to understand motility and spatial properties of hPSCs in culture, achieved through computational tracking in order to answer key questions about human cell development. Students will be expected to present their findings orally at a research day in York in September 2024.