Gene expression at single cell resolution (single cell RNA-sequencing)
Single cell RNA-sequencing (scRNAseq) has become a popular tool for capturing and profiling the gene expression patterns (transcriptome) of individual cell types from heterogenous tissues such as human pancreatic islets. With this technology, for example, we can investigate the transcriptomes of thousands of individual pancreatic islet cells!
A common application of scRNAseq is characterizing the unique gene expression profiles of different cell types. Below is an example of scRNAseq data from human pancreatic islets projected into 3-dimensional t-SNE (t-distributed stochastic neighbor embedding) space. In the animation below, we can see that each cell type (each point represents an individual single cell and each color represents a different cell type) clusters distinctly from each other, suggesting their gene expression profiles to be very different.
Using scRNAseq to classify pancreatic islet cell types
With scRNAseq, we have determined there to be at least 4 different pancreatic islet cell types: beta (red), alpha (blue), delta (green), and gamma/PP (purple), each with very distinct transcriptome profiles (Panels A and B in the figure below). A closer look at the heat map and violin plots in Panel C show that each different cell type demonstrates robust and unique expression for certain genes (e.g., INS, NKX6-1, and ADCYAP1 expression are highest in beta (red) cells).
If you’re interested in learning more about scRNAseq and its applications in human pancreatic islets, please check out this paper: