Vidya Chandrasekaran Saint Mary's College of California

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Genomics at Saint Mary's College of California

Course Overview

I incorporated GEP material as part of the laboratory section for an existing Genetics course (Bio 105). The course had mainly juniors and seniors and lab meets 4 hours a week for 13 weeks. The lab began with a tour of the JGI's sequencing facility to understand the process of DNA sequencing. This was followed by two weeks of demo of finishing using the practice datasets for finishing. We installed Consed and students went through the finishing exercise. This was followed by a lecture on BLAST and introduction to annotation tools and the simple BLAST lab exercises that are posted on the Wiki. The students were assigned the more detailed BLAST exercises on the Drosophila annotation as homework assignements which we discussed the following lab. The students then did a practice annotation on D. erecta before being assigned their fosmid. The students worked in pairs and annotated either genes from the dot chromosome of D. erecta or D.mojavensis.


Bio 105 course information

Genetics Laboratory Handbook (BIO 105L)

The materials for this lab were developed as part of the curriculum by the Dr. Sarah Elgin at Washington University at Saint Louis for the Genomics Education Partnership (GEP).

Description:

This lab is designed to give students exposure to genomic tools that are publicly available and also get students involved in genomics based research that will be incorporated into the public databases. This lab will start with a visit to the genome sequencing facility at the Joint Genome Institute in Walnut Creek, where we will learn about sequencing the genome. The next two labs will be focused on how a genome is finished following the shotgun genome project. In these two labs, we will work on finishing exercises and use a UNIX based program called Consed. The remaining labs are devoted to assigning genes onto the finished sequence. This step is called annotation of the DNA sequence. In this portion of the lab, we will be annotating parts of the Drosophila genome. In addition to the annotation, we will explore the number of repeats present in the genome and identify any novel repeats as well as look at synteny between the different Drosophila species.

Grading:

The labs will be graded based on reports and presentation (40% of total grade):

Written report on individual fosmid : 10
Oral Presentation on the individual fosmid: 15
Assignments and Exercises: 10
Lab work and participation: 5


Lab policies:

a) No net surfing, checking email during lab hours on the computers
b) No eating, drinking in lab
c) No plagiarism.


Syllabus for Bio105

Bio 105 syllabus is available for download.