Total RNA-Seq in KSHV lytic reactivation model with RNA ligase depletion
iSLK-BAC16 cells were transfected with siRNAs pools targeting human RNA ligases (RLIG1, RTCB) or a nontargeting control (NTC). At 24 hours post transfection, iSLK-BAC16 were induced with 1 ug/mL Doxycycline, 1 mM Sodium Butyrate in 1x DMEM media supplemented with 2% Tet-approved FBS. 0 hour time point was when induction media was added and cells were first placed at 37 degrees Celsius to incubate. Total RNA was collected at 3 days post induction using the Direct-zol RNA MiniPrep Kit. ERCC spike-in controls were added to total RNA. RNA was ribominus selected and directional cDNA libraries were generated. 2 biological replicates were sequenced for all samples. Sequencing was performed using the Illumina NovaSeq platform to generate 150 bp PE reads.