Example of ChIP-chip results. Results from ChIPs of S. cerevisiae histone H3 and Flag-H2B, plotted by intergenic genomic loci as a function of the percentile rank of the transcription rate in the downstream genes (Bernstein et al. 2004). An inverse relationship can be seen between nucleosome occupancy (as represented by enrichment for histone H3 and H2B) and promoter strength, as indicated by the transcription rate. These ChIP samples were amplified with the DNA linear amplification protocol introduced here. (Reprinted with permission from Bernstein et al. [2004].)