Jessica Holder, M.S. Candidate

Department of Biological Sciences 

"Identifying Alternatively Spliced Events and Exons Between Blood Cells"

Advisory Committee Members

• Mira Han, Ph.D., Advisory Committee Chair
• Jingchun Chen, Ph.D., Advisory Committee Member
• Matthew Meiselman, Ph.D., Advisory Committee Member
• Lukasz Sznajder, Ph.D., Graduate College Representative

Abstract

Transcript isoforms arising from alternative splicing events can contribute to the development of a cell’s identity and function and overall protein diversity. Peripheral blood is a useful model to study and evaluate computational methods for alternative splicing detection due to its
abundant data across various sequencing protocols. The alternative splicing events across different blood cell types have not been completely identified and detecting alternative splicing through short read sequencing is still a challenging problem. Here, we propose to integrate multiple bulk RNA-seq datasets of purified blood cells using a novel integration method
to identify the cell-type specific alternative splicing events in different blood cell types. We applied the detection methods to two data sets across two cell type comparisons. We show that we can integrate the results of two independent approaches of alternative splicing detection that were previously considered too different to be reconciled. The results show
little concordance between the different approaches, but allowed us to be more confident in the events identified as they were commonly detected by both approaches and datasets. The integration allowed us to re-analyze past studies and produce a comprehensive list of alternatively spliced events based on multiple softwares. In the future, we plan to broaden the cell type comparisons and provide a ground truth for the single cell level alternative splice analysis.