K8 CLIP-Seq in KSHV reactivated BCBL-1 cells

KSHV K8 is required for KSHV DNA replication and is found to be an RNA binding protein. To understand the molecular mechanism of K8 in regulation of DNA replication, we examine the binding RNAs of K8 protein in BCBL-1 cells using CLIP-Seq analysis. Overall design: KSHV K8 CLIP was performed in TPA-induced BCBL-1 cells. K8-immunoprecipitation of UV cross-linked K8-RNA complexes, followed by RNA isolation, library construction, and high-throughput sequencing (Illumina HiSeq 2500); we performed 2 biological replicates, three technical replicates of each biological replicate. Technical replicates were pooled before library construction. The two biological replicates for the IgG and BJAB samples did not produce enough material for sequencing each replicate independently so they were combined into a single sample each for IgG and BJAB.