Sally Lee / Dr. Thomas J. Fahey - Week 7

Week 7 - A journey through my mini project

Name: Sally Lee

Clinician mentor: Dr. Thomas J. Fahey


On Tuesday (7/18), I presented my Immersion mini research project titled 'Generation of scRNA-seq profiles of human islets to study pancreatic neuroendocrine tumors.' The primary focus of this project was to analyze scRNA-seq profiles of pancreatic neuroendocrine tumors (pNET). However, I encountered several challenges to make progress on the project. 

One significant obstacle was that I am not yet added to the IRB protocol, which meant I could not collect patient samples myself. This limitation forced me to consider alternative solutions. Moreover, pNET patients are relatively rare, making it difficult to gather a sufficient number of samples for analysis. Another challenge was the lack of available scRNA-seq data in Drs. Fahey and Finnerty’s lab that I could use for comparison with my established control dataset.


Fortunately, I had a productive meeting on Thursday (7/19) with Drs. Fahey, Finnerty, and my PI, Dr. Chen. We discussed potential strategies to move forward and overcome these hurdles. Dr. Fahey will be connecting me with his residents, who are responsible for collecting tumor specimens. This way, whenever new pNET patient samples become available, I will be alerted and can incorporate them into my analysis. Additionally, Dr. Finnerty offered bulk RNA-seq data of pNET from previous analyses. I am excited about this opportunity as it opens up new avenues for exploration. However, I must admit that I have limited experience in combining bulk and single-cell datasets. Nonetheless, I plan to look into this data thoroughly to identify potential analyses I can perform using my control dataset. The idea of pseudobulk analysis is particularly intriguing, and I am eager to research more about it.


As I continue on this research journey, I am reminded that setbacks and challenges are natural parts of the process, and each hurdle we overcome will brings us closer to making a difference in the lives of patients affected by pNETs. I am excited about this collaboration and where this project will lead us in the future. 

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