ChIP-chip of KSHV DNA. Chromatin immunoprecipitation (ChIP) was performed as described  using an antibody to the phosphorylated form of histone H3 and DNA was directly labeled with Cy3-dCTP or Cy5-dCTP. (A) ChIP of uninduced BCBL-1 cells. BCBL-1 cells were cultured normally and a ChIP was performed as described in Materials and Methods. All amplicons are listed at the bottom of the panel. (B) ChIP of induced BCBL-1 cells. BCBL-1 cells were induced with 0.3 mM sodium butyrate for 48 hrs and ChIP was performed as described. All amplicons are listed at the bottom of the panel. (C) Summary of ChIP results from uninduced and induced BCBL-1 cells. Only the KSHV amplicons are shown. The blue bars are hybridizations from uninduced cells while the red bars are hybridizations from induced cells. Below the graph is a schematic of the KSHV genome indicating the location and direction of transcription of the ORFs. ORFs indicated in white were not included in the analysis as the corresponding amplicons were not properly amplified for printing.