RNA-seq and data analysis.

Total RNA was prepared from iSLK-BAC16 cells treated with and without Dox (1 μg/ml) and soluble HIV Tat (0.2 μg/ml) and from HMEC1 cells transduced with or without LINC00313 in the presence and absence of HIV Tat (0.2 μg/ml) using TRIzol (Invitrogen; catalog no. 15596018). Paired-end 100-bp high-throughput RNA sequencing (RNA-seq) was performed by the sequencing core facility of the cancer progression research center at National Yang-Ming University using Illumina HiSeq 2000. The raw reads were aligned to human reference genome GRCh38/Hg38. Transcript levels were expressed as reads per kilobase of transcript per million mapped reads (RPKM) with mRNA and lncRNA information obtained from RefSeq82 and NONCODE v5.0, respectively, using the Partek Genomics Suite. The lncRNAs IDs from NONCODE v5.0 were converted into RefSeq IDs using NONCODE ID conversion (http://www.noncode.org/id_conversion.php). Differential expression of mRNAs and lncRNAs was analyzed by comparing RPKM and calculated as fold change. To determine the expression profile similarity between KSHV reactivation and HIV Tat treatment, iSLK-BAC16 cells treated with and without Dox (1 μg/ml) and soluble HIV Tat (0.2 μg/ml) were analyzed by hierarchical clustering using dChip software. The differential expressed mRNAs were subjected to disease and function analysis using Ingenuity Pathway Analysis software (Qiagen).