Transcriptome analysis for LMP1 depletion rescue with Wildtype LMP1 or individual TES mutant LMP1 in GM12878 Lymphoblastoid cell line (LCL)

RNA-seq was used to characterize the LMP1 mediated regulation of host target gene regulation. Here, we stably expressed doxycycline-induced HA-tagged wildtype (WT) LMP1 or TES1 mutant (TES1m) oe TES2 mutant(TES2m) in GM12878 LCL. We then depleted LMP1 from these cells using CRISPR-Cas9 approach and treated the cells with 400ng/ml of doxycycline to induce expression of WT, TES1m or TES2m LMP1 to rescue from the LMP1 depletion mediated effects (including loss of cell viability) to understand and differenciate the role of LMP1 TES1 vs TES2 domains in LCL. Overall design: Comparative gene expression profiling analysis of RNA-seq data in GM12878 LCL upon rescue of CRISPR-Cas9-mediated LMP1 depletion with induced expression of wildtype LMP1, TES1mutant LMP1or TES2m LMP1. The GM12878 LCL substituting LMP1 depletion with stable expression of wildtype LMP1 was used as the control.