Exploring the sea urchin genome with undergraduates using bioinformatic tools.

It is important to provide undergraduate students with research experiences so that they obtain essential problem-solving skills and come to appreciate the process of science whether or not they pursue graduate study. However, such experiences can be difficult to achieve at a primarily undergraduate institution where time and resources are limited. One strategy is to incorporate research into the laboratory component of courses, with students having input into the specific topic being investigated. In this chapter, we present a series of activities that can be brought together as a semester or year-long project after students select a gene with the potential to be analyzed in a novel species of echinoderm. Students become acquainted with important databases, software programs, and online tools as they clone their gene, confirm its identity through alignment with homologous sequences, and characterize its expression through both qPCR and WMISH. We provide streamlined protocols that allow the work to be accomplished in an efficient manner, and conclude with ideas for assignments that can be completed in parallel to improve students' writing and oral communication skills in preparation for any career.