A comparative analysis of DNA barcode microarray feature size

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.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.Genome-wide studies often measure changes in the abundance of all gene products over a period of time or under varying conditions. Microarrays have made these studies possible by enabling researchers to monitor all known genes of an organism simultaneously to detect patterns of gene activity [1], alternative splicing variants [2] the presence of single nucleotide polymorphisms [3], the presence of copy number variants and [4] DNA binding sites of diverse proteins [5], among others. One application of microarrays that our laboratory has focused on is the parallel identification of individual molecular barcoded gene deletion mutants grown competitively in pools [6,7]. Through the efforts of the Yeast Deletion Consortium, a Yeast KnockOut (YKO) collection was constructed consisting of approximately 6,000 heterozygous gene deletions (>96% of all annotated open reading frames), of which over 1,100 are known to be essential for growth [7]. The remaining ~5,000 genes are nonessential, created as homozygous deletions and MATαand MATα deletion collections. These collections were made by systematic replacement o