Department: Bioengineering
Faculty Advisor(s): Kun Zhang

Primary Student
Name: Jeffrey A Gole
Email: jgole@ucsd.edu
Phone: 858-822-3635
Grad Year: 2013

Humans host trillions of microbial cells which have interesting interactions with their hosts. Recently, the entire genomes of these single bacterial cells have been amplified for sequencing analysis. The current methods for single cell genome amplification are very low throughput and highly biased, ultimately wasting thousands of dollars in reagents and materials. Currently, our lab is creating new methods to allow for unbiased, high throughput amplification. By designing PDMS microwell arrays, it is possible to have up to 4,000 reactions on a platform no bigger than a microscope slide. Trapping single cells in individual wells ensures that there is no crossover amplification. The template cells have been successfully amplified in microwells using whole genome amplification methods such as multiple displacement amplification (MDA), and the amplicons have been visualized growing in real time through fluorescent monitoring. Low input library construction and subsequent sequencing have shown a genomic library that proves significantly less biased than previously published single cell libraries. These accomplishments will ultimately allow for facilitated single cell genome reconstruction and will mitigate the waste of sequencing resources.

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