Pathogenic Influenza Viruses and Coronaviruses Utilize Similar and Contrasting Approaches To Control Interferon-Stimulated Gene Responses

Menachery, Vineet D.; Eisfeld, Amie J.; Schäfer, Alexandra; Josset, Laurence; Sims, Amy C.; Proll, Sean; Fan, Shufang; Li, Chengjun; Neumann, Gabriele; Tilton, Susan C.; Chang, Jean; Gralinski, Lisa E.; Long, Casey; Green, Richard; Williams, Christopher M.; Weiss, Jeffrey; Matzke, Melissa M.; Webb-Robertson, Bobbie-Jo; Schepmoes, Athena A.; Shukla, Anil K.; Metz, Thomas O.; Smith, Richard D.; Waters, Katrina M.; Katze, Michael G.; Kawaoka, Yoshihiro; Baric, Ralph S.

To determine the histone modification distribution, quantitative realtime PCR was performed targeting the 5=UTR (Ϫ750 bp-TSS [region 750 base pairs upstream of the transcriptional start site]) of select genes; target and primer information is included in the supplemental material. ChIP results were reported as fold difference (or differential occupancy), allowing comparison across multiple samples. For this, each sample was normalized to the input and then the fold enrichment was calculated using the ⌬⌬C T method. The fold difference for each gene was determined by dividing the appropriate time-matched mock by the experimental group. Finally, the fold difference values were converted to log 2 and plotted. Data presented are the means Ϯ standard errors for triplicate samples.