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BMC Genomics. 2009 Oct 13;10:471. doi: 10.1186/1471-2164-10-471.

A comparative analysis of DNA barcode microarray feature size.

Author information

  • 1Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.

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 microm features sizes independently identified the primary target of tunicamycin to be ALG7.

CONCLUSION:

We show that the data obtained with 5 microm feature size is of comparable quality to the 30 microm size and propose that further shrinking of features could yield barcode microarrays with equal or greater resolving power and, more importantly, higher density.

PMID:
19825181
[PubMed - indexed for MEDLINE]
PMCID:
PMC2765990
Free PMC Article

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