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

Emily Oldham and Dan Pierce ('03)

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

Layout of our DNA Microarray


Experimental Design

Need Stronger Signal

3DNA Dendrimer Advantage = 300+ dyes per binding





DNA Concentrations Printed



Establish Scanning Parameters



Concentrations Alters Ratios


Sequence-Specific Variations


Altered 3DNA Sticky Ends


Wanted to Improve Quality of Signal: Clone PCR Products

Original PCR Products
Cloned PCR Products


Clean Up Printed DNA: Clone PCR Products


Optimized Experimental Conditions: Signal Up and Noise Down


Plasmids Improve Signal



What about Other Ratios? 10:1, 3:1, 1:1, 1:3, 1:10
(expected log2 = 3.3, 1.6, 0, -1.6, -3.3)



Good Trends

ACS Workshop

Genomics Course

Biology Department

Send comments, questions, and suggestions to: macampbell@davidson.edu or (704) 894 - 2692
© Copyright 2004 Department of Biology, Davidson College, Davidson, NC 28035