a, Spike-in ChIP-seq with drosophila chromatin shows importance of per-cell normalization to account for global changes in the fraction of the ChIP antibody target bound to chromatin. The decrease in dm3 reads, as compared to hg19 reads, reflective of an increase in the total quantity of H3K27ac decorating human the human cancer cell genome (RH4) increasing upon HDAC inhibition (left). The shape of SE metagene plots are shown without normalization to Spike in reads (middle) or with the normalization to Spiked-in chromatin (right; shading indicates the SEM). b, HDACi induced increase of H3K27ac, BRD4 and YY1 (as measured by ChIP-Rx) at CTCF anchors surrounding SEs in RH4 cells. Shading shows the SEM of the ChIP-seq signal. c, HDACi induced increased background levels of BRD4 and YY1 binding, outside called peaks. d, Chromatin-associated factors (RAD21 of cohesin, HDAC2/3, p300, BRD4, YY1), RNA Pol2, accessibility (ATAC-seq) and H3K27ac altered by acute (6 hr) inhibition of HDAC with Entinostat. Ground-state ChIP-Rx levels at insulators, enhancers and gene bodies near super enhancers are indicated with dashed lines (DMSO), and Entinostat treated ChIP-Rx levels shown in solid lines. Details regarding the number of independent replicate experiments is provided in the Statistics and Reproducibility section of the Methods.