Challenges of building a single cell atlas
Thousands of single cell RNA-sequencing studies have generated data from multitudes of human donors. There is now the opportunity to combine this data into a single resource with enormous power to test for tissue- and disease-specific cell states and better understand homeostasis and its disruption. We are therefore assembling a single cell atlas of mucosal tissues to identify differences in how epithelium and immune cells interact with the outside world. However, there are major challenges in this work. Barriers to data availability, inconsistent publishing and sharing standards, poor annotation and description of workflows, and constantly updated dry lab protocols mean that a single cell RNA-sequencing study published five years ago is irreconcilably different from one published now. Here, I will discuss these challenges and why it is worth addressing them.
Bio
I completed my undergraduate degree at the University of Queensland in 2019 before beginning my PhD with Associate Professor Ashraful Haque at the University of Melbourne, located in the Peter Doherty Institute, where I studied CD4+ T cell differentiation and interaction with myeloid and non-immune cells with spatial transcriptomics. I then undertook a postdoc with Associate Professor Arutha Kulasinghe at UQ Frazer Institute using multiplexed proteomics to find predictors of relapse in a large breast cancer cohort. I am currently located at QIMR Berghofer under the supervision of Dr Amanda Oliver in the Barrier Immunity lab where we are attempting to understand how and why epithelial cells present antigen to immune cells.
