ChIP assay was performed using protocol from Dr. Farnham’s laboratory (https://bohdan-khomtchouk.github.io/docs/Chromatin-Immunoprecipitation-ChIPs-Protocol-from-Farnham-Lab.pdf ). Chromatin DNA prepared from 1 × 107 TREx-MH-K-Rta-shKDM4A-Flag-KDM4A-WT and -KDM4A-K471R cells was used for ChIP assays using anti-KDM4A rabbit polyclonal antibody (25 (link)) and rabbit nonimmune serum IgG (Alpha Diagnostic International). Sequencing libraries were prepared using 10 ng of purified ChIP DNA using Illumina HiSeq Rapid PE Cluster Kit v2 (Illumina, TG-403-2001) according to the manufacturer’s instruction and analyzed by paired-end Illumina HiSeq 2000 sequencing. ChIP-Seq data were aligned to the human reference genome (GRCh38) and HHV-8 reference genome (NC_009333.1 ) by Partek Flow (Partek).
ChIP DNA was confirmed for successful IP using SYBR Green-based real-time qPCR analysis in the CFX Connect real-time PCR detection system (Bio-Rad). The specific primer set (5′-TTAGAGCGTTTCCAGACCT-3′ and 5′-GAGGATTCAACAGTGATGGGAC -3′) was designed to amplify the potential KDM4A binding site on the IL-10 promoter.
ChIP DNA was confirmed for successful IP using SYBR Green-based real-time qPCR analysis in the CFX Connect real-time PCR detection system (Bio-Rad). The specific primer set (5′-TTAGAGCGTTTCCAGACCT-3′ and 5′-
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