Remote research: A bioinformatics adventure for undergraduates - Casey Schmidt

Описание: Presentation by Casey Schmidt (Emory University) at #Dros21. Learn more about the conference: https://genetics-gsa.org/drosophila/​

Numerous studies have demonstrated the value of involving undergraduates in laboratory research. However, access to research labs is often limited by available space and time. To reach a larger population of students, many faculty have incorporated portions of their research into Course-based Undergraduate Research Experiences (CUREs). CUREs provide authentic research experiences to a much larger number of students than traditional apprenticeship models, and their inclusion in biology curricula is becoming much more widespread. Although the COVID-19 pandemic prevented our undergraduates from physically working in the lab, it provided us an opportunity to pilot a bioinformatics-based CURE based on our current work. The Rieder lab is interested in factors that regulate the Drosophila histone genes, and our undergraduates engaged in a search for new regulators using publicly available high-throughput datasets. Because the Drosophila histone locus is a repetitive array, any sequencing reads mapping to this region are normally discarded. To address this issue, we used a custom genome containing a single copy of the locus. We first engaged our four experienced undergraduate laboratory members in background discussions and literature searches, and they formed hypotheses and chose candidate proteins. Next, we guided students to find high-throughput ChIP-seq datasets in NCBI GEO and taught them to map the reads to the histone gene array using Galaxy, a free web-based platform that integrates many bioinformatics tools. After mapping, the students visualized their data using the open source Integrative Genomics Viewer (IGV) software. Strikingly, all four students discovered proteins that are enriched at the Drosophila histone array. Some of the students will be performing follow-up bioinformatics experiments in the spring (for example, mapping available RNA-seq datasets). We are repeating this program with a group of naive students to expand our research and obtain more diverse feedback. Our approach solved the accessibility issue exacerbated by the COVID-19 pandemic, is completely free, and presents an opportunity for more accessible and inclusive access to undergraduate research.