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Massively Multiplexed DNA Sequencing with Ultrahigh-throughput Droplet Microfluidics


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,


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