A comparison of high density oligonucleotide and PCR-based array platforms for chIP chip in yeast

ChIP chip data was obtained for the factors Tec1, Ste12 and Sok2 in S. cerevisiae using high density oligonucleotide arrays. This data was then compared to results obtained previously for the same factors under the same growth conditions but using spotted PCR arrays (Borneman et al Genes Dev 2006). This showed the high density arrays to be more reproducible using fewer numbers of replicates. In addtion, the high density arrays provided increased accuracy, sensitivity and reproducibity when compared to the PCR arrays. Keywords: ChIP-chip ChIP chip was performed for three factors, Tec1, Ste12 and Sok2. For each factor, 3 biological replicates were performed, with one replicate for each factor treated as a dye swap.