MDI Biological Laboratory

COVID-19-Mediated Gene Expression Patterns: UMF, UMFK & UMPI

A short course for students from the UMaine campuses at Farmington, Fort Kent, and Presque Isle.


In this era of Big Data, the volume of biological data is growing exponentially. Systematic profiling and analysis of these data will provide new insight into the biology and human health. Among diverse types of biological data, gene expression data most closely mirror both the static phenotypes and the dynamic changes in biological systems. In this short course, students will learn how gene expression data is both generated and analyzed using RNA-sequencing (RNA-seq) techniques. Students will analyze published RNA-seq data generated from SARS-CoV-2 infections to understand how coronavirus infection changes gene expression patterns in model animals, organoid cultures, and human patients. Additional hands-on training will focus on the fundamentals of cell culture work, including cell seeding, counting, and media changes. Cell cultures will be analyzed for specific gene activity using immunofluorescence and light microscopy.

At the end of this course, students will be able to:

  • Identify genes with altered expression levels changes upon SARS-CoV-2 infection
  • Know how to use web and Linux-based bioinformatics tools
  • Work successfully with cell cultures using proper aseptic technique
  • Design an experiment based on the result of computational analysis


About the Maine INBRE program

This short course is supported and organized by the Maine IDeA Network of Biomedical Research Excellence (INBRE).

Maine is one of 23 states that have been identified by the National Institutes of Health as having historically received low levels of NIH funding. The INBRE program was established to strengthen research networks in each of these states, so that they could become more competitive for federal research grants. In Maine, our network is comprised of 14 institutions, with the MDI Biological Laboratory as the lead institution. Other institutions in our network include the following: Bates College, Bowdoin College, Colby College, College of the Atlantic, the Honors College at the University of Maine, the Jackson Laboratory, Southern Maine Community College, the University of Maine, UMaine Farmington, UMaine Fort Kent, UMaine Machias, UMaine Presque Isle, and the University of New England.

Money from Maine INBRE supports research training experiences like this short course, as well biomedical research and laboratory facilities throughout our network. Other training experiences include academic year and summer student research. Please check with the INBRE contact at each institution for the most accurate information about opportunities on your campus. At UMaine Farmington, that contact is Jean Doty. At UMaine Fort Kent, that contact is Nicole Boudreau. At UMaine Presque Isle, that contact is Jason Johnston.


This research training opportunity is supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P20GM103423.

The IDeA program builds research capacities in states that historically have had low levels of NIH funding by supporting basic, clinical and translational research; faculty development; and infrastructure improvements.