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2009 GCAT Microarray Workshops
Workshop #1 July 6 - 10
Morehouse College, Atlanta, GA

This will be the last GCAT Microarray Workshop

Workshop #1

Link to Workshop #2

Schedule Overview

Instructors:

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

 

Day 1 (Monday July 6)

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

10:15 - 10:30 Short Break Dr. Pleez B. Prompt
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 - 1:15 Lunch  
1:15 - 1:45 Practice Layout and Gene List Laurie Heyer & Consuelo Alvarez
1:45 - 2:30 Addressing and Gridding Laurie Heyer & Consuelo Alvarez
2:30 - 2:45 Short Break  
2:45 - 3:15 Practice Gridding Laurie Heyer & Consuelo Alvarez
3:15 - 4:00 Segmentation Laurie Heyer & Consuelo Alvarez
4:00 - 4:30 Practice Segmentation Laurie Heyer & Consuelo Alvarez
4:30 - 5:00 Generate Multiple Ratio Expression Files Laurie Heyer & Consuelo Alvarez
5:00 -6:00

Practice Multiple Ratio Expression Files

Quit MAGIC Tool

Laurie Heyer & Consuelo Alvarez
Goal for Day 1: Create 6 Columns of Data
6:00 onwards Dinner  

Schedule Overview

Day 2 (Tuesday July 7)

Time
Activity
Lead Instructors
8:30 - 11:00 cDNA prep with provided RNA (get started right away) Anne Rosenwald & Todd Eckdahl
  Introductions and overviews (during incubation) Anne Rosenwald & Todd Eckdahl
  get the slides ready for the first hybridization mix Anne Rosenwald & Todd Eckdahl
11:00 - 11:30 RNA degradation using NaOH Anne Rosenwald & Todd Eckdahl
11:30 - 12:00 cDNA concentration Anne Rosenwald & Todd Eckdahl
12:00 - 12:30 Prepare hybridization mix 1 to go on arrays for overnight incubation Anne Rosenwald & Todd Eckdahl
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

Generate cDNA Probes & Hybe Them on Chips

6:00 - 7:30 Dinner  
7:30 - 8:30

Synthetic Biology Presentation

 Malcolm Campbell & Todd Eckdahl

Schedule Overview

GCAT Wet Lab Protocols

Day 3 (Wednesday July 8)

Time
Activity
Lead Instructors
8:30 - 9:30 Washes, and set up 2nd hybridization mix Anne Rosenwald & Todd Eckdahl
8:30 - 12:30 Second hyb begins Anne Rosenwald & Todd Eckdahl
  prep RNA from frozen pellets with Ambion kit Anne Rosenwald & Todd Eckdahl
  Run some on gels Anne Rosenwald & Todd Eckdahl
12:30 - 1:30 Lunch  
12:30 - 5:30 Wash and scan chips Anne Rosenwald & Todd Eckdahl
  Discussion of Quantifying
mRNA Levels with RT PCR 		Anne Rosenwald & Todd Eckdahl
  Discussion of Using Microarrays in Courses
Spot Synthesizer 		Anne Rosenwald & Todd Eckdahl
  Discussion of Using Microarrays in Research Anne Rosenwald & Todd Eckdahl
  Discussion of Results Anne Rosenwald & Todd Eckdahl

Goal for Day 3: Wash & Scan Chips

Discuss and Trouble Shoot Results
6:00 - 7:00 Dinner  
7:30 - 8:30 Evolution Lecture by Ken Miller, HHMI-produced DVD  

 

GCAT Wet Lab Protocols

Schedule Overview

Day 4 (Thursday July 9)

Time
Activity
Lead Instructors
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

SOP for MAGIC Tool

Laurie Heyer & Consuelo Alvarez
3:00 - 3:15 Short Break  
3:15 - 6:00

Correlation Exercise (Directions and Excel Examples)

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 Presentation by Sally O'Connor and Claudia Rankins

Sally 1 (overview)
Claudia (focused on a few areas)
Sally 2 (Writing a better proposal)

Schedule Overview

Day 5 (Friday July 10)

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

2009 Workshop 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.

GCAT Home Page

© Copyright 2009 Department of Biology, Davidson College,
Send comments, questions, and suggestions to: macampbell@davidson.edu