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Access Type

WSU Access

Date of Award

January 2018

Degree Type

Thesis

Degree Name

M.S.

Department

Molecular Biology and Genetics

First Advisor

Francesca Luca

Second Advisor

Roger Pique-Regi

Abstract

Complex traits and diseases are associated with variants in non-coding regions of the genome. These variants have shown to alter phenotypes as well. Characterizing these variants is therefore important and more recently has been made possible with high throughput reporter assays like STARR-seq. A novel method developed in our lab, BIT-STARR-seq based on STARR-seq is able to further identify allele-specific expression in synthesized oligos representing regulatory regions in the DNA while using unique molecular identifiers to account for PCR duplicates. In this study, we optimize the library preparation protocol for BiT-STARR-seq for the HUVEC cell line using the STARR-seq human plasmid. We test the efficiency of the protocol and troubleshoot problems we came across. Finally, we sequence 5 replicates of the newly generated library and quantify their presence in transformed cells.

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