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Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
 
BMC Genomics. 2009; 10: 471.
Published online Oct 13, 2009. doi:  10.1186/1471-2164-10-471
PMCID: PMC2765990
A comparative analysis of DNA barcode microarray feature size
Ron Ammar,#1,2,3 Andrew M Smith,#1,2,3 Lawrence E Heisler,3,4 Guri Giaever,1,3,4 and Corey Nislowcorresponding author1,2,3
1Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
2Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
3Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
4Department of Pharmaceutical Sciences, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
corresponding authorCorresponding author.
#Contributed equally.
Ron Ammar: ron.ammar/at/utoronto.ca; Andrew M Smith: am.smith/at/utoronto.ca; Lawrence E Heisler: l.heisler/at/utoronto.ca; Guri Giaever: ggiaever/at/gmail.com; Corey Nislow: corey.nislow/at/gmail.com
Received March 25, 2009; Accepted October 13, 2009.
Abstract
Background
Microarrays are an invaluable tool in many modern genomic studies. It is generally perceived that decreasing the size of microarray features leads to arrays with higher resolution (due to greater feature density), but this increase in resolution can compromise sensitivity.
Results
We demonstrate that barcode microarrays with smaller features are equally capable of detecting variation in DNA barcode intensity when compared to larger feature sizes within a specific microarray platform. The barcodes used in this study are the well-characterized set derived from the Yeast KnockOut (YKO) collection used for screens of pooled yeast (Saccharomyces cerevisiae) deletion mutants. We treated these pools with the glycosylation inhibitor tunicamycin as a test compound. Three generations of barcode microarrays at 30, 8 and 5 μm features sizes independently identified the primary target of tunicamycin to be ALG7.
Conclusion
We show that the data obtained with 5 μm feature size is of comparable quality to the 30 μm size and propose that further shrinking of features could yield barcode microarrays with equal or greater resolving power and, more importantly, higher density.
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