UC San Diego

The advent of high throughput single cell genomic technologies has revolutionized the study of cell biology. It has enabled scientists to discover rare cell types that were hidden in gene expression measurements of bulk cell populations. This led to many discoveries in complex tissues made up of heterogeneous cell populations, notably the mammalian brain. However, cells function in coordination with their environment and neighboring cells. Because these high throughput single cell technologies dissociate the cells from their native tissue, the spatial context is lost. In situ methods that examine cells in fixed tissue have existed for decades and are used routinely by doctors to diagnose diseases. But those traditional in situ methods do not have the capability to measure the expression of more than a handful of genes necessary to correlate with single cell. Presented here is one in situ approach for highly multiplexed RNA quantification that is also the first to be successfully used in human cortical sections, to the best of our knowledge.

The first chapter of my dissertation covers the development of DARTFISH, a method that enables highly multiplexed in situ digital quantification of targeted RNA transcripts in fresh frozen tissue.

The second chapter describes efforts to map cell types identified by single-cell or single-nuclei RNA sequencing to spatially defined cells from DARTFISH cortical sections.

The third and final chapter details ongoing improvements to DARTFISH to achieve better cell type classification of single cells in DARTFISH.