Publication Date

Spring 2022

Degree Type

Master's Project

Degree Name

Master of Science in Bioinformatics (MSBI)

Department

Computer Science

First Advisor

Wendy Lee

Keywords

Differential expression, microRNA, RNA-Seq, Shiny

Abstract

ABSTRACT Thrombosis in the internal jugular vein (IJV) has been identified as a risk factor for astronauts undergoing spaceflight, following a 2019 study in which one astronaut developed a thrombus, and several others experienced stagnant or retrograde blood flow. To better understand this phenomenon, a model that simulates the effects of microgravity on blood flow in the IJV is being developed. mRNA and microRNA NGS sequencing will be used to study the transcriptome of human umbilical vein endothelial cells (HUVEC) in simulated microgravity conditions. A microRNA sequencing (miRNA-seq) pipeline has been developed to quantify the miRNA sequencing results. A graphical user interface for differential expression analysis of miRNA read count data, identification of genes targeted by the miRNAs, and gene set analysis has also been developed. Data from an experiment which sequenced both miRNA and mRNA is processed using the pipeline and Shiny app.

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