A Comparison of Drosophila Melanogaster RNA-seq Data Sets

Wednesday, June 2, 2021

10:00 AM-12:00 PM

BIOMED Master's Thesis Defense
 
Title:
A Comparison of Drosophila Melanogaster RNA-seq Data Sets

Speaker:
Roze Alzabey, MS Candidate
School of Biomedical Engineering, Science and Health Systems
Drexel University

Advisor:
Catherine von Reyn, PhD
Assistant Professor
School of Biomedical Engineering, Science and Health Systems
Drexel University

Details:
RNA sequencing (RNA-seq) has been established as a high throughput sequencing method that provides gene expression profiling. However, with the vast amount of data generated through RNA-seq, it remains a challenge to extract meaningful interpretations of the data. In addition, RNA-seq library preparation requires multiple steps, and there remains to be differences in techniques at various levels of the process, and a lack of standardized methods to compare across different datasets.

In this project, we ask the question of how well do RNA-seq data of the same cell type compare across two different labs utilizing different steps in the sequencing protocol. We first validate the reproducibility of the data by comparing the replicates within each dataset using correlation analysis. We then compare across the two datasets to 1) establish a standardized technique to compare across RNA-seq libraries, 2) highlight the differences generated when certain steps of the library preparation process are different, 3) verify the correlation between specific cell types, as published RNA-seq data are currently being used as a reference to classify cell types with single cell RNA-seq data (scRNA-seq). The model organism we use is Drosophila melanogaster, due to the availability of advanced genetic techniques and its well-established anatomical model.

Contact Information

Natalia Broz
njb33@drexel.edu