Bio343: Laboratory Methods In Genomics
Spring, 2017
A. Malcolm Campbell (he/him/his)

Tentative Syllabus

Class meets T/R 9:40 - 10:55 pm in Wall B05
Office Hours: M 11-noon; T 3 - 4 pm; or most anytime by appointment

Learning Goals

• Students will experience gene expression analysis of RNAseq data.
• Students will appreciate the amount of subjectivity involved in genomics research.
• Students will understand how genomics is a suite of tools that spans the small/big biology divide.
  

Learning Objectives

1. Define terms used in RNA sequencing and assembly. (knowledge)
2. Describe a gene based on in-depth analysis of a genome. (comprehension)
3. Report your findings to the class verbally and to a wider audience in writing. (comprehension)
4. Explain how transcriptomes reveal which parts of the genome are activated. (comprehension)
5. Demonstrate computer skills used in modern genomics. (application)
6. Examine different signaling pathways that lead to cell and tissue growth. (analysis)
7. Test whether a known pathway is activated in experimental tissue compared to control. (analysis)
8. Collect and integrate published data with RNAseq data to describe Down Syndrome. (synthesis)
9. Evaluate data quality and completeness of signaling pathway activation. (evaluation)
10. Assess the objectivity and subjectivity used in genomic research. (evaluation)
    

Bio343 is a lab-only course that is primarily data analysis by computer. I am very excited about this course for three main reasons.

1. We will be working on an inherently interesting question - Down Syndrome. We will be looking at the transcriptome of mouse embryonic stem cells (ES) that have an extra copy of the mouse ortholog of chromosome #21 which causes Down Syndrome. In particualr, we will be looking at two different populations of cells. One population will have the father's extra copy of "chromosome #21". The other popuation wil have the mother's extra chromosome. Will we see any differences in the transcriptomes of these two different sources of ES?
2. We will be collaborating with a class from Colby College in Maine; Dr. Andrea Tilden will be offering a parallel course for her students. We will benefit from collaborating with her students as we conduct our research because both classes will exchange information that could be of interest to everyone. This collaboration mirrors modern research in the post-genomics era.
3. We are also collaborating with Drs. Charlie Wray and Laura Reinholdt at Jackson Laboratory in Bar Harbor, ME. We are part of an educational pilot experiment to see if it is feasible to offer research experiences to a national network of undergraduates using RNAseq data to answer legitmate research questions. Very few students in the world get to answer an interesting biological question using RNAseq data and you are among the few who will get this experience.

Because this is a research course, we will all have to be flexible in the material we learn. It is impossible to know where this course will take us exactly. I have a rough plan, but nothing firm yet until we see how these projects unfold. If you need a highly structured course, this will not be a good fit for you. Each student will need to learn how to edit a wiki site used for this research project.

Student Collaborators

Required Readings

1) Online web sites

2) Research publications on genomes (PDFs gathered during semester)

3) Course wiki site

Tentative Weekly Schedule

Grading
Grades will be based on:

• research summary Word File (solo author) email to Dr. C. (10% total grade)
  
• group oral presentation #1 (10% total grade)
• status report (solo author; 20% total grade)
• group oral presentation #2 (20% total grade)
• peer review on 2 oral presentations (each review is 5% total grade)
• peer review of draft term paper (review is 5% total grade)
• term research paper solo author (25% total grade)

The exact nature of the presentations and papers cannot be determined at this point. You will use the course wiki page as an online lab notebook to track your daily progress. Keep in mind that your work will be the foundation that investigators will use for subsequent research so it is important to keep good notes online.

Genomics Lecture Course

Genomics Minor

Biology Department

© Copyright 2017 Department of Biology, Davidson College, Davidson, NC 28035
Send comments, questions, and suggestions to: macampbell@davidson.edu