Annotation of the Kaposi’s Sarcoma-Associated Herpesvirus Transcriptome Using Cross-Platform Sequencing

The transcriptome of Kaposi's sarcoma associated herpesvirus (KSHV, or Human gammaherpesvirus 8) was sequenced on ONT MinION and Illumina platform to obtain the differential gene expression profile of the virus and the KSHV-positive primary effusion lymphoma cell line (iBCL1-3xFLAG-RTA) as host. KSHV-positive cells were cultured in either normoxic or hypoxic conditions. RNA was isolated before and after reactivation of the virus in triplicates. Oxford Nanopore Technologies MinION platform was used to obtain full length transcripts. Illumina CAGE-Seq was also used to analyse the transcription start sites of viral and cellular transcipts.