ChIP-seq analysis of KSHV Rta

Briefly, chromatin DNA from 1 × 10⁸ TREx- K-Rta BCBL-1 cells were used per assay and immunoprecipitated with 20 µg mouse anti-FLAG M2 (Sigma-Aldrich, F1804) or mouse control IgG (Santa Cruz Biotechnology, sc2025). 1 ng ChIP-enriched or input DNA was used to generate Illumina-compatible libraries with the KAPA LTP Library Preparation Kit (Kapa Biosystems, KR0453) according to the manufacturer’s recommendations. Libraries were submitted for sequencing (50-bp single read) on an Illumina HiSeq 2500 sequencing system. The ChIP-Seq data was aligned to the human hg19 reference genome assembly and reference KSHV genome sequence (Human herpesvirus 8 strain JSC-1 clone BAC16, GenBank: GQ994935.1) with Bowtie 2^{61 (link)}. Peak finding was performed with the MACS2 (Model-based Analysis of ChIP-Seq 2) program^{64 (link)} according to the standard parameters described in the developer’s manual. We used the default settings with a minimum FDR (q-value) cutoff of 0.05. The peaks and reads alignments were visualized using the Integrative Genomics Viewer (IGV) genome browser from the Broad Institute.