In Spring 2005 I designed a genetics lab curriculum
which included DNA sequencing and analysis as an experiential learning project.
As of 2008, almost 800 genetics students have participated in genome sequencing,
hundreds of thousands of bases of DNA have been sequenced, and our first
chloroplast genome has been completed (Tall Fescue, GenBank FJ466687, picture
below, manuscript
submitted).
The curriculum is constantly evolving but the most useful version has been to include the project as a set of three lessons. The lessons were created as an addendum/complement to the lab manual we have adopted, "Genetic Investigations for the Laboratory" Rebecca Seipelt, Deborah Clark, Phillip Mathis, 4th ed., McGraw-Hill Companies, Inc.
This curriculum assumes that a shotgun (or equivalent) library of the genome at hand has been prepared ahead of time and individual clones/plasmids are brought into the lab as bacterial cultures. Shotgun libraries introduce an unknown element into the lab on top of the experiential aspect. Even though the library is screened ahead of time for fidelity, no one knows (not even the instructor) what each student will find when the clone is sequenced. I find this an exciting element and I look forward to this portion of the semester every year.
Lesson/Week 1 - Purification of the clone/plasmid from the bacterial culture. This lesson is sometimes taught in conjunction with another DNA extraction lesson from the lab manual.
Lesson/Week 2 - Lesson/Week 2 - DNA quantification and setting up sequencing reactions. This lesson is taught as an addendum to an electrophoresis lesson from the lab manual. We set up sequencing reactions using Beckman-Coulter's QuickStart sequencing kit used with their CEQ-8000 genetic analyzer.
Lesson/Week 3 - DNA analysis. This lab guides students through a series of BLAST searches.
I hope these labs are useful and if you have any questions please write to me at acahoon@mtsu.edu.