DIP-chip from Cbf1, Leu3, Pho2, Pho4, Rap1, Rox1, and Swi5

DNA Immunoprecipitation was performed using purified, naked, genomic DNA and purified recombinant DNA binding domains for S. cerevisiae transcription factors (Cbf1, Leu3, Pho2, Pho4, Rap1, Rox1, and Swi5) and then competitively hybridized against input DNA on NimbleGen 385k whole-genome, 32bp, tiling arrays to identify the consensus sequence for each transcription factor as a whole in the genome. Each protein was used for 2 independent replicates at a protein concentration of 40nM. The second replicate is a dye-swap. During analysis, regions of the genome had to be identified as bound in both replicates as well as the average of the two replicates to be considered true binding sites.