The ability to conduct and read-out assays in high-throughput is a powerful tool
for studying complex biological systems. For example, fluorescence activated cell
sorting, which enables high-throughput assays of cellular markers on single cells by
fluorescent staining has been instrumental to understanding the immune system.
Although fluorescence can be a powerful readout for high-throughput assays, it also has
significant drawbacks. First, a fluorescent assay must be available for the target of
interest, and second, only a few different assays can be used at once, owing to the
limited spectrum available to fluorophores and detectors. In my dissertation, I develop a
novel method of high-throughput assay readout using massively parallel DNA
sequencing and droplet microfluidics. By conducting assays inside picoliter sized
droplets generated using microfluidic channels, molecular biology assays that generate
nucleic acids as a readout can be performed at kHz throughput. By uniquely barcoding
the nucleic acids in each droplet, the results of each individual assay can be read in
parallel using in a massively parallel sequencer. With this approach, I develop a method
of deep sequencing single molecules and a method of sequencing single cell genomes
at low-coverage, to generate highly accurate and haplotyped long DNA sequence reads
and characterize diverse microbial populations in an unprecedented manner,
respectively.
