Laboratory Methods In Genomics

Spring, 2007

A. Malcolm Campbell


Tentative Syllabus: Bio 343 Laboratory Methods in Genomics

Student Collaborators

Course Goals

1) Learn how to conduct a DNA microarray experiment from beginning to end. They will design the microarray layout, print enough chips for their experiments, perform the experiments, analyze their data and present their findings. This project will be a new one with the potential to publish our findings. We will try to measure the genomic response in E. coli to the ground breaking repressilator.

2) Validate microarray data using quantitative PCR (qPCR) with the department's Real-Time PCR machine.

3) Develop student-friendly and complete protocols for all aspects of their research.

4) Communicate orally the complex procedures and datasets.

5) Write a manuscript for submission to an appropriate journal, based on the semester's work.

 

Required Readings

1) Biography of Seymour Benzer - Time, Love, Memory by Jonathan Weiner (Knopf Press, NY, 1999). You can get a good price from Amazon.com.

2) Reprints from research journals

3) Protocols for this course


Tentative Weekly Schedule

Week of Semester
Subject Matter
Week 1:
Aug 24 & 25

Discuss Semester-Long Research Plans & Set Educational Goals

Pre-Semester Assessment

Read Microarray chapter and Repressilator section

Grow repressilator cells

Plan experimental design

Week 2:
Aug 31 & Sep 1

Learn how to design a microarray; print buffer alone
(PDF or Word version)

Learn how to regulate repressilator

Design repressilator chip

Purify and clone DNAs

Week 3:
Sep 7 & 8

Print repressilator chip

Week 4:
Sep 14 & 15

Continue repressilator chip production

MAGIC Tool Overview

Week 5:
Sep 21 & 22

Learn how to produce E. coli probes

Learn MAGIC Tool (Image Processing)

Week 6:
Sep 28 & 29

Begin experiments

Learn MAGIC Tool (Data Analysis)

Week 7:
Oct 5 & 6

Continue experiments

Analyze data

Week 8:
Oct 12 & 13

Continue experiments

Analyze data

Watch first 4 videos on qPCR (requires free registration)

 

Week 9:
Oct 19 & 20

Continue experiments

Analyze dat

Work with RT-PCR Machine

Week 10:
Oct 26 & 27

Analyze Data

Week 11:
Nov 2 & 3

Analyze Data

Design PCR Primers

Week 12:
Nov 9 & 10

Validate Microarray Data

Week 13:
Nov 16 & 17

Continue Data Collection

Thanksgiving Next Week

Week 14:
Nov 30 & Dec 1

Analyze Data

Week 15:
Dec 7

Final Report


Grading
Grades will be based on lab participation (20%), lab notebooks (20%), experimental design (20%), research paper (20%), and oral presentations (20%). The exact nature of the final paper cannot be determined at this point. The GCAT assessment tool will be used as a pre/post measure of overall learning gains in the various phases of DNA microarray experiments. Lab notebooks will be collected and evaluated each Friday after presentations.

Grading Scale:

Conversion of Percentages to Letter Grades
A = 100 - 95 A- = 94 - 92
B+ = 91 - 89 B = 88 - 86 B- = 85 - 83
C+ = 82 - 80 C = 79 - 77 C - = 76 - 74
D+ = 73 - 71 D = 70 - 68
F = < 67

Genomics Concentration

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© Copyright 2008 Department of Biology, Davidson College, Davidson, NC 28035
Send comments, questions, and suggestions to: macampbell@davidson.edu