Genomic analyses of Loc1, Puf6, and Khd1 binding patterns and transcriptional effects

We performed ChIP-chip of Loc1, Puf6, and Khd1 in order to determine the genetic loci they bind. We repeated these experiments with lighter fixation in the presence and absence of RNase to determine whether these associations are via DNA or RNA (analysis shows that they associate with the loci via the RNA). We also performed transcriptional profiling of knd1- and puf6- cells to determine if the binding of each factor has significant effects on the mRNA abundances of its targets (no significant transcriptional effects were observed). Each analyzed dataset comes from independently-produced triplicate samples, with one dye-swap performed for each dataset.