Download Microarray Cancer Lab - Madison West High School

DNA Chips (Microarrays - see Animation)
Lab Experiment
What does Smoking do to my Genes?
Observe lung tissue from smokers and nonsmokers
LAB Overview
1. Print DNA Chip
1.5. (Teacher) Bake (20-80 min ~ 80°C)
2. Wash (4 x 2 min in SDS and water)
3. Hybridize with Target DNA (room temp ~ 20 min)
4. Wash (4 x 2 min in SDS and salt solutions)
5. Send to Scanning Facility
6. Analyze - bioinformatics tools
Make a DNA Chip
Lab Step 1 - DNA Chip Printing
Probe DNA
1 microliter spots of DNA in solution
Each grid: 11 genes in
duplicate
DNA Chip Terminology
Probe DNA - short pieces of single stranded DNA
attached to glass
Target DNA - cDNA from cells grown under
different conditions
Floating in solution on top of probe DNA
example: cDNA from seedlings grown in light vs. dark
5
Probe DNA - attachment to Glass Slide
Treated slide
From Telechem International
Hybridization
Probe (Chip) DNA + Target cDNA (Simulated)
~20 minutes room temp
Costly
Microarray Technology Considerations
•One Array ~ $400. Not including Tissue Preparation
•One array can cost >$1000.
•Scanning equipment >$50-200,000.
Complicated - each step requires controls for
validation and replicates for reliability
•Harvesting Tissue
•Preparing Chip and Tissue
•Hybridizing
•Analyzing
•Software is complicated and expensive
•Huge data sets
•Requires sophisticated statistical analysis
WE NEED HIGHLY SKILLED PEOPLE!
• Physicists
Develop instrumentation
• Chemists
develop chip printing, target labeling and Hybridization
• Biologists
Tissue growth and harvesting; interpretation of results
•Computer scientists and statisticians
software development and validation