Week 7: Seo-Ho/Dr. Thomas Fahey

Much of this seventh week was spent polishing my analysis of pancreatic neuroendocrine tumor (PNET) spatial transcriptomic data. Compared to the earlier weeks of Immersion, when I had no idea where to start, I have become much more comfortable with the analysis workflow with the help of my fellow lab members. After annotating various clusters by cell type, a process that can be pretty subjective and ends up resulting in multiple ways of annotating too choose from, I was able to see how tumor regions, fibrotic regions, and non-tumor regions differ by their cell-type and genetic makeup. Some of the major data points of this analysis include cell type/region fraction by pathology, top expressed genes by sample and pathology, and enriched gene ontology biological processes based on pathology and the presence of vascular invasion. Over the next few weeks, I will be continuing to refine my cell type annotations and performing literature review into potential gene driver candidates of metastasis and PNET initiation to continue investigating from a wet lab angle.

My first round of human embryonic stem cell to monocyte differentiation finished this week, and I performed flow cytometry for the first time using CD14 as a marker. While my live percentage of cells was around 50% (I suspect this is because the cells grew quite confluent and kept many of the dead cells were stuck to the bottom of the well), the percentage of CD14+ cells from those live cells was ~87%, indicating successful differentiation. The next steps include playing around with seeding densities to see if I can maintain a higher viability. My second round of differentiation will be done next week, so I look forward to those results!

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