2007 GCAT Microarray Workshops
Two Sessions; 20 people per session
Time and Location TBA
Workshop #2
Instructors:
Consuelo Alvarez, Errol Archibold, Malcolm
Campbell, Todd Eckdahl,
Edison Fowlks, Charles Hauser, Laurie Heyer, Dave Kushner, and Anne Rosenwald.
Time |
Activity |
Lead Instructors |
| Prior to Lunch | Last Minute Laptop Preparation | Laurie Heyer and Malcolm Campbell |
| 12:00 - 1:00 | Lunch | Eat at Cafeteria |
| 1:15 - 1:45 | Greetings and Overview | Edison Fowlks |
| 1:45 - 2:15 | Introduction to Microarrays, MAGIC Tool web, Raw Data Launch |
Malcolm Campbell David Kushner |
| 2:15 - 2:30 | Short Break | Dr. Pleez B. Prompt |
| 2:30 - 3:15 | Making a Project | Dave Kushner and Laurie Heyer |
| 3:15 - 3:35 | Practice Making Projects | Dave Kushner and Laurie Heyer |
| 3:35 - 4:15 | Slide Layout and Gene List | Dave Kushner and Laurie Heyer |
| 4:15 - 4:45 | Practice Layout and Gene List | Dave Kushner and Laurie Heyer |
| 4:45 - 5:15 | Gridding | Dave Kushner and Laurie Heyer |
| 5:15 - 6:00 | Practice Gridding | Dave Kushner and Laurie Heyer |
Goals for Day 1: Learn MAGIC Tool Prepare Tiff Files for Quantification |
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| 6:00 - 7:00 | Dinner | Eat at Cafeteria |
| 7:00 - 8:00 | NSF Presentations in Lecture Room II in Nabrit/Mapp/McBay Hall | TBA |
Day 2 (July 19) Wednesday
Time |
Activity |
Lead Instructors |
| 7:30 - 8:30 | Breakfast | Eat at Cafeteria |
| 8:30 - 9:30 | Refresher and Segmentation | Dave Kushner and Laurie Heyer |
| 9:30 - 10:00 | Practice Segmentation | Dave Kushner and Laurie Heyer |
| 10:00 - 10:30 | Generate Multiple Ratio Expression Files | Dave Kushner and Laurie Heyer |
| 10:30 - 10:45 | Short Break |
Dr. B. Ohn Thyme |
| 10:45 - 11:15 | Log Transforming Data | Dave Kushner and Laurie Heyer |
| 11:15 - 11:30 | Practice Log Transforming Data | Dave Kushner and Laurie Heyer |
| 11:30 - 12:00 | Gene Information |
Dave Kushner and Laurie Heyer |
| 12:00 - 12:15 | Practice Gene Information | Dave Kushner and Laurie Heyer |
| 12:15 - 1:15 | Lunch Break | Eat at Cafeteria |
| 1:15 - 2:30 | Explore Data | Dave Kushner and Laurie Heyer |
| 2:30 - 2:45 | Short Break | Dr. Don T Linger |
| 2:45 - 3:15 | Practice Exploring | Dave Kushner and Laurie Heyer |
| 3:15 - 4:15 | Clustering (you practice later: online + PDF) | Dave Kushner and Laurie Heyer |
| 4:15 - 6:00 | Flexible Catch Up Time | GCAT Instructors |
Goal for Day 1: Manipulate and Explore Data Start Wet Lab Process |
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| 6:00 - 7:00 | Dinner | Eat at Cafeteria |
| 7:00 - late | Trouble Shooting and Practice Session Available | GCAT Instructors |
Day 3 (July 20) Thursday
Time |
Activity |
Lead Instructors |
| 7:30 - 8:00 | Breakfast | Eat at Cafeteria |
8:00 - 8:30 |
Overview of Wet Lab |
Todd Eckdahl and Anne Rosenwald |
8:30 - 9:15 |
Set up Reverse Transcription and Cy-Dye Incorporation |
Todd Eckdahl and Anne Rosenwald |
9:15 - 10:30 |
Discussion DeRisi Experiment, RNA Isolation, Quality Control |
Todd Eckdahl and Anne Rosenwald |
10:30 - 10:45 |
Short Break |
Dr. Don T Linger |
10:45 - 11:15 |
Discussion of Labeling Alternatives |
Todd Eckdahl and Anne Rosenwald |
11:15 - 11:45 |
RNA Degradation |
Todd Eckdahl and Anne Rosenwald |
11:45 - 12:15 |
Purification of cDNA |
Todd Eckdahl and Anne Rosenwald |
12:15 - 12:45 |
Lunch Break |
Eat at Cafeteria |
12:45 - 1:30 |
Discussion of Quantifying mRNA Levels with RT PCR |
Todd Eckdahl and Anne Rosenwald |
1:30 - 2:00 |
Measurement of Labeling Efficiency |
Todd Eckdahl and Anne Rosenwald |
2:00 - 2:30 |
Prehybridization Procedures |
Todd Eckdahl and Anne Rosenwald |
2:30 - 3:00 |
Labeled Sample Preparation and Hybridization |
Todd Eckdahl and Anne Rosenwald |
3:00 - 3:15 |
Short Break |
|
3:15 - 4:15 |
Discussion of Using Microarrays in Courses |
Todd Eckdahl and Anne Rosenwald |
4:15 - 5:15 |
Discussion of Using Microarrays in Research |
Todd Eckdahl and Anne Rosenwald |
Goal for Day 4: Set Up Microarray Hybridizations |
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6:00 - 7:00 |
Dinner |
Eat at Cafeteria |
7:00 - late |
Trouble Shooting and Practice Session Available |
GCAT Instructors |
Day 4 (July 21) Friday
Time |
Activity |
Lead Instructors |
| 7:30 - 8:00 | Breakfast | Eat at Cafeteria |
| 8:00 - 9:00 | Posthybridization Washing | Todd Eckdahl and Anne Rosenwald |
| 9:00 - 10:30 | Microarray Slide Scanning | Todd Eckdahl and Anne Rosenwald |
| 10:30 - 10:45 | Short Break |
|
| 10:45 - 12:15 | Discussion of Results | Instructors and Participants |
| 12:15 - 1:15 | Lunch Break | Eat at Cafeteria |
| 1:15 - 135 | Refresh Memory | Dave Kushner and Laurie Heyer |
| 1:35 - 3:00 | Generate Ratios from Your Microarray | Dave Kushner and Laurie Heyer |
| 3:00 - 3:15 | Short Break | Dr. Kum Bak Soon |
| 3:15 - 6:00 | 1 Column Exploration | Dave Kushner and Laurie Heyer |
Goal for Day 4: Wash, Scan and Trouble Shoot Chips Know what to do after wet lab! |
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| 6:00 - 7:00 | Dinner | Eat at Cafeteria |
| 7:00 - late | Trouble Shooting and Practice Session Available | GCAT Instructors |
After Dinner Discussions and Assessment
Time |
Activity |
Lead Instructors |
| 7:00 - 7:30 | Summarize Workshop | GCAT Instructors |
| 7:30 - 8:30 | Discuss Curriculum Ideas | GCAT Instructors |
| 8:30 - 10:00 | Your Quesitons | GCAT Instructors |
Goal for Day 4: Know how you
can adapt and adopt GCAT
resources. |
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Day 5 (July 22) Saturday
Time |
Activity |
Lead Instructors |
| 7:30 - 8:00 | Breakfast | Eat at Cafeteria |
| 8:00 - 10:15 | Make a Series from Separate 1 Columns | Dave Kushner and Laurie Heyer |
| 10:15 - 10:30 | Short Break | Dr. Juan Las Time |
| 10:30 - 12:00 | DeRisi Data Analaysis |
Dave Kushner and Laurie Heyer |
| 12:00 - 12:30 | Workshop Assessment | You! |
| 12:30 - 1:00 | Lunch Break | Eat at Cafeteria |
Goal for Day 5: Increase your
confidence with microarrays! |
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See photos from 2003 workshops
© Copyright 2006 Department of Biology, Davidson College,
Davidson, NC 28035
Send comments, questions, and suggestions to: macampbell@davidson.edu
