Experimental Design and Controls

Experimental Design Questions

Define probe v. target
Label RNA v. cDNA (impact on spotted material)
Cy series v. Alexa series dyes
Spots made of oligos v. cDNA
Affymetric chips v. printed glass chips
Reproducibility within and between labs


Dye reversal
Pooled v. control reference mRNA
Control spots from another species

Our Research

How do you know if what you are measuring accurately represents your sample?

Layout of our DNA Microarray


Calibrated Acquisition of Fluorescence


Tested Concentration of Spotted Materials (4,102 fold range)


Unexpected Gene-specific Variation


Compared Three Detection Variations



Wanted to Improve Quality of Signal: Clone PCR Products

Original PCR Products
Cloned PCR Products


Optimized Experimental Conditions: Signal Up and Noise Down


What about Other Ratios? 10:1, 3:1, 1:1, 1:3, 1:10

Good Trends

CSU Workshop

Genomics Course Page

Biology Department Main Page

Send comments, questions, and suggestions to: macampbell@davidson.edu or (704) 894 - 2692
© Copyright 2003 Department of Biology, Davidson College, Davidson, NC 28035