Click to see a larger version of this image.

2007 GCAT Microarray Workshops
Two Sessions; 20 people per session
Week of July 8 - 14: Morehouse College

Workshop #2

Link to Workshop #1

Schedule Overview

Instructors:

Consuelo Alvarez, Malcolm Campbell, Todd Eckdahl,
Edison Fowlks, Laurie Heyer, Dave Kushner, and Anne Rosenwald

Day 1 (July 10)

Time
Activity
Lead Instructors
Prior to Lunch Last Minute Laptop Preparation Dave Kushner and Laurie Heyer
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, Online Tutorials

Launch

Malcolm Campbell
(quick links to short and long animations)

David Kushner
2:15 - 2:30 Short Break Dr. Pleez B. Prompt
2:30 - 3:15 Making a Project Dave Kushner
3:15 - 3:35 Practice Making Projects Dave Kushner
3:35 - 4:15 Slide Layout and Gene List Dave Kushner
4:15 - 4:45 Practice Layout and Gene List Dave Kushner
4:45 - 5:15 Addressing and Gridding Dave Kushner
5:15 - 6:00 Practice Gridding Dave Kushner

Goals for Day 1: Learn MAGIC Tool

Prepare Tiff Files for Quantification

6:00 - 7:00 Dinner Eat at Cafeteria
7:30 - 8:30 Genomics Speaker
Nabrit/Mapp/McBay Hall, Lecture Room II 		Cancelled for Medical Reasons

Schedule Overview

Day 2 (July 11)

Time
Activity
Lead Instructors
7:30 - 8:30 Breakfast Eat at Cafeteria
8:30 - 9:30 Refresher and Segmentation Dave Kushner
9:30 - 10:00 Practice Segmentation Dave Kushner
10:00 - 10:30 Generate Multiple Ratio Expression Files Dave Kushner
10:30 - 10:45

Short Break

 Dr. B. Ohn Thyme
10:45 - 11:15 Log Transforming Data Dave Kushner
11:15 - 11:30 Practice Log Transforming Data Dave Kushner
11:30 - 12:00

Gene Information

Dave Kushner
12:00 - 12:15 Practice Gene Information Dave Kushner
12:15 - 1:15 Lunch Break Eat at Cafeteria
1:15 - 2:30 Explore Data Dave Kushner
2:30 - 2:45 Short Break Dr. Don T Linger
2:45 - 3:15 Practice Exploring Dave Kushner
3:15 - 4:15 Clustering (you practice later: online + PDF) Dave Kushner
4:15 - 6:00 Flexible Catch Up Time GCAT Instructors
 

Goal for Day 2: Manipulate and Explore Data

Start Wet Lab Process

 
6:00 - 7:00 Dinner Eat at Cafeteria
7:00 - 8:00 NSF Speakers
Sally O'Connor and Diane Okamuro - NSF Program Officers

 

Schedule Overview

GCAT Wet Lab Protocols

Day 3 (July 12)

Time

Activity

Lead Instructors

7:30 - 8:00 Breakfast Eat at Cafeteria

8:00 - 8:30

Overview of Wet Lab

Consuelo Alvarez

8:30 - 9:15

Set up Reverse Transcription and Cy-Dye Incorporation

Consuelo Alvarez

9:15 - 10:30

Discussion DeRisi Experiment, RNA Isolation, Quality Control

Consuelo Alvarez

10:30 - 10:45

Short Break

Dr. Don T Linger

10:45 - 11:15

Discussion of Labeling Alternatives

Consuelo Alvarez

11:15 - 11:45

RNA Degradation

Consuelo Alvarez

11:45 - 12:15

Purification of cDNA

Consuelo Alvarez

12:15 - 12:45

Lunch Break

Eat at Cafeteria

12:45 - 1:30

Discussion of Quantifying mRNA Levels with RT PCR

Consuelo Alvarez

1:30 - 2:00

Measurement of Labeling Efficiency

Consuelo Alvarez

2:00 - 2:30

Prehybridization Procedures

Consuelo Alvarez

2:30 - 3:00

Labeled Sample Preparation and Hybridization

Consuelo Alvarez

3:00 - 3:15

Short Break

3:15 - 4:15

Discussion of Using Microarrays in Courses
Spot Synthesizer

Consuelo Alvarez

4:15 - 5:15

Discussion of Using Microarrays in Research

Anne Rosenwald et al.

Goal for Day 4: Set Up Microarray Hybridizations

6:00 - 7:00

Dinner

Eat at Cafeteria
7:30 - 8:30 Synthetic Biology Presentation
Nabrit/Mapp/McBay Hall, Lecture Room II 		GCAT Faculty
PPT Slides

GCAT Wet Lab Protocols

Schedule Overview

Day 4 (July 13)

Time
Activity
Lead Instructors
7:30 - 8:00 Breakfast Eat at Cafeteria
8:00 - 9:00 Posthybridization Washing Consuelo Alvarez
9:00 - 10:30 Microarray Slide Scanning Consuelo Alvarez
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
1:35 - 3:00 Generate Ratios from Your Microarray Dave Kushner
3:00 - 3:15 Short Break Dr. Kum Bak Soon
3:15 - 6:00 1 Column Exploration Dave Kushner

Goal for Day 4: Wash, Scan and Trouble Shoot Chips

Know what to do after wet lab!
6:00 - 7:00 Dinner Eat at Cafeteria

 

Schedule Overview

Day 5 (July 14)

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
10:15 - 10:30 Short Break Dr. Juan Las Time
10:30 - 12:00

DeRisi Data Analaysis

Dave Kushner
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!

Schedule Overview


Email Edison Fowlks or Malcolm Campbell with Questions

Link to Workshop 2007 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

Biology Home Page

© Copyright 2007 Department of Biology, Davidson College, Davidson, NC 28035
Send comments, questions, and suggestions to: macampbell@davidson.edu