ORF57 eCLIP of KSHV lytic reactivation in iSLK-BAC16 model

Subconfluent monolayers of iSLK-BAC16 were induced for 24 hours with 1 ug/mL Doxycycline, 1 mM Sodium Butyrate in 1x DMEM media supplemented with 2% Tet-approved FBS. The eCLIP assays were performed by Eclipse Bioinnovations following the protocol detailed in van Nostrand et al. (Nat Methods 13, 508-514, 2016). For these assays, two independent biological replicates were performed using an affinity purified anti-ORF57 polyclonal antibody (Sei et al. PLOS Path, 2015; Sei and Conrad Virology 2011). An IgG control antibody was tested in parallel, but the yield from this was low, so all subsequent comparisons were performed relative to the size-matched input control.