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2008 GCAT Microarray Workshops
Two Sessions; 20 people per session
Week of July 14 - 19: California State University - Fullerton


Workshop #2

Link to Workshop #1

Schedule Overview

Instructors:

Consuelo Alvarez, Malcolm Campbell, Todd Eckdahl,
Edison Fowlks, Laurie Heyer, Charles Hauser, and Anne Rosenwald

Day 1 (Tuesday July 15)

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
(quick links to short and long animations)

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
6:00 - 7:30 Dinner  
7:30 - 8:30

Dr. Animesh Ray from Keck Graduate Institute
Room: Humanities 110

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)

Schedule Overview

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

 
6:00 - 7:00 Dinner Eat at Cafeteria
7:30 - 8:30

Dr. Laura Hoopes from Pomona College
Room: Humanities 110

Success with Students

 

Schedule Overview

GCAT Wet Lab Protocols

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

6:00 - 7:00 Dinner  
7:30 - 8:30 NSF Program Officers
Room: Humanities 110

NSF Funding Opportunities

GCAT Wet Lab Protocols

Schedule Overview

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!
6:00 - 7:00 Dinner  
7:30 - 8:30 NSF Program Officers

NSF Funding Opportunities

 

Schedule Overview

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.

Schedule Overview

 



Email Edison Fowlks or Malcolm Campbell with Questions

Link to Workshop 2008 Main Page

This material is based upon work supported by the National Science Foundation under Grant No. DBI-0627478. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

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