Laboratory Methods In Genomics
Spring, 2007
A. Malcolm Campbell
Tentative Syllabus: Bio 343 Laboratory Methods in Genomics
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 Read Microarray chapter and Repressilator section Grow repressilator cells Plan experimental design |
Week 2: |
Learn how to design a microarray; print
buffer alone 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: |
Continue experiments Analyze data Watch first 4 videos on qPCR (requires free registration)
|
Week 9: |
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:
| 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 |