2008 GCAT Microarray Workshops
Two Sessions; 20 people per session
Week of July 14 - 19: California State University - Fullerton
Workshop #2
Schedule Overview
Instructors:
Consuelo Alvarez, Malcolm
Campbell, Todd Eckdahl,
Edison Fowlks, Laurie Heyer, Charles Hauser, and Anne Rosenwald
Time |
Activity |
Lead Instructors |
| 8:00 - 8:30 | Last Minute Laptop Preparation | Laurie Heyer and Malcolm Campbell |
| 8:30 - 9:00 | Greetings and Overview | Edison Fowlks |
| 9:00 - 10:15 | Introduction to Microarrays, MAGIC Tool web, Raw Data, Online Tutorials Launch |
Malcolm Campbell Laurie Heyer & Consuelo Alvarez |
| 10:15 - 10:30 | Short Break | |
| 10:30 - 11:15 | Making a Project | Laurie Heyer & Consuelo Alvarez |
| 11:15 - 11:35 | Practice Making Projects | Laurie Heyer & Consuelo Alvarez |
| 11:35 - 12:15 | Slide Layout and Gene List | Laurie Heyer & Consuelo Alvarez |
| 12:15 - 1:30 | Lunch | |
| 1:30 - 4:00 | cDNA prep with provided RNA (get started right away) | Charles Hauser & Anne Rosenwald |
| Introductions and overviews (during incubation) | Charles Hauser & Anne Rosenwald | |
| get the slides ready for the first hybridization mix | Charles Hauser & Anne Rosenwald | |
| 4:00 - 4:30 | RNA degradation using NaOH | Charles Hauser & Anne Rosenwald |
| 4:30 - 5:00 | cDNA concentration | Charles Hauser & Anne Rosenwald |
| 5:00 - 5:30 | Prepare hybridization mix 1 to go on arrays for overnight incubation | Charles Hauser & Anne Rosenwald |
Goal for Day 1: Start MAGIC
Tool Start Wet Lab |
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| 6:00 - 7:30 | Dinner | |
| 7:30 - 8:30 | Dr. Animesh Ray from Keck Graduate Institute |
Research with Microarrays |
| 8:30 - 9:30 | Reception hosted by Steve Murray (College of Natural Science and Mathematics) |
Garden Café with light
snacks/beer/wine (a short walk from Humanities) |
Day 2 (Wednesday July 16)
Time |
Activity |
Lead Instructors |
| 8:00 - 8:30 | Practice Layout and Gene List | Laurie Heyer & Consuelo Alvarez |
| 8:30 - 9:15 | Addressing and Gridding | Laurie Heyer & Consuelo Alvarez |
| 9:15 - 9:45 | Practice Gridding and Break if you need one | Laurie Heyer & Consuelo Alvarez |
| 9:45 - 10:30 | Segmentation | Laurie Heyer & Consuelo Alvarez |
| 10:30 - 11:00 | Practice Segmentation | Laurie Heyer & Consuelo Alvarez |
| 11:00 - 11:30 | Generate Multiple Ratio Expression Files | Laurie Heyer & Consuelo Alvarez |
| 11:30 - 12:30 | Practice Multiple Ratio Expression Files |
Laurie Heyer & Consuelo Alvarez |
| 12:30 - 1:30 | Lunch | |
| 1:30 - 2:00 | Log Transforming Data | Laurie Heyer & Consuelo Alvarez |
| 2:00 - 2:15 | Practice Log Transforming Data | Laurie Heyer & Consuelo Alvarez |
| 2:15 - 2:45 | Gene Information |
Laurie Heyer & Consuelo Alvarez |
| 2:45 - 3:00 | Short Break and Practice Gene Information | |
| 3:00 - 4:00 | Explore Data | Laurie Heyer & Consuelo Alvarez |
| 4:00 - 4:30 | Practice Exploring | Laurie Heyer & Consuelo Alvarez |
| 4:30 - 5:30 | Clustering Overview (you practice later: online + PDF) | Laurie Heyer & Consuelo Alvarez |
Goal for Day 2: Manipulate and Explore Data |
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| 6:00 - 7:00 | Dinner | Eat at Cafeteria |
| 7:30 - 8:30 | Dr. Laura Hoopes from Pomona College |
Success with Students |
Day 3 (Thurday July 17)
Time |
Activity |
Lead Instructors |
| 8:30 - 9:30 | Washes, and set up 2nd hybridization mix | Charles Hauser & Anne Rosenwald |
| 8:30 - 12:30 | Second hyb begins | Charles Hauser & Anne Rosenwald |
| prep RNA from frozen pellets with Ambion kit | Charles Hauser & Anne Rosenwald | |
| Run some on gels | Charles Hauser & Anne Rosenwald | |
| 12:30 - 1:30 | Lunch | |
| 12:30 - 5:30 | Wash and scan chips | Charles Hauser & Anne Rosenwald |
| Discussion of Quantifying mRNA Levels with RT PCR |
Charles Hauser & Anne Rosenwald | |
| Discussion of Using Microarrays in Courses Spot Synthesizer |
Charles Hauser & Anne Rosenwald | |
| Discussion of Using Microarrays in Research | Charles Hauser & Anne Rosenwald | |
| Discussion of Results | Charles Hauser & Anne Rosenwald | |
Goal for Day 3: Wash & Scan Chips Discuss and Trouble Shoot Results |
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| 6:00 - 7:00 | Dinner | |
| 7:30 - 8:30 | NSF Program Officers Room: Humanities 110 |
NSF Funding Opportunities |
Day 4 (Friday July 18)
Time |
Activity |
Lead Instructors |
| 8:00 - 8:30 | Refresh Memory | Laurie Heyer & Consuelo Alvarez |
| 8:30 - 10:15 | Generate Ratios from Your Microarray | You |
| 10:15 - 10:30 | Short Break |
|
| 10:30 - 12:15 | 1 Column Exploration | Laurie Heyer & Consuelo Alvarez |
| 12:15 - 1:15 | Lunch | |
| 1:15 - 3:00 | Make a Series from Separate 1 Columns | Laurie Heyer & Consuelo Alvarez |
| 3:00 - 3:15 | Short Break | |
| 3:15 - 6:00 | DeRisi Data Analaysis | Laurie Heyer & Consuelo Alvarez |
Goal for Day 4: Know what to
do after wet lab! |
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| 6:00 - 7:00 | Dinner | |
| 7:30 - 8:30 | NSF Program Officers | NSF Funding Opportunities |
Day 5 (Saturday July 19)
Time |
Activity |
Lead Instructors |
| 8:00 - 8:30 | Summarize Past 4 Days | GCAT Instructors |
| 8:30 - 10:15 | Discuss Curriculum Ideas | GCAT Instructors |
| 10:15 - 10:30 | Short Break |
Dr. Juan Las Time |
| 10:30 - 12:15 | Your Quesitons and Workshop Assessment | GCAT Instructors |
| 12:15 - 1:15 | Lunch and depart | Eat at Cafeteria |
Goal for Day 5: Know how you
can adapt and adopt GCAT resources. |
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© Copyright 2008 Department of Biology, Davidson College,
Davidson, NC 28035
Send comments, questions, and suggestions to: macampbell@davidson.edu
