Complete in vivo SHAPE-MaP structure of the SARS-CoV-2 genome

SHAPE-MaP structure probing experiment was performed on SARS-CoV-2 infected Vero cells at 4 days post infection with two biological replicates. For each replciate, SHAPE-MaP includes a sample treated with 2-methylnicotinic acid imidazolide acid (modified) or a minue reagent (unmodified). NAI preferentially reacts with unpaired bases in RNA, forming acylated bases. These modifications are encoded as mutation during reverse transcripatse and library preparation. After sequencing and alignment, the reactivity profiles of 'modified' and 'unmodified' samples are used to calculate SHAPE reactivity of each base SHAPE-MaP on SARS-CoV-2 genomic RNA growing in Vero cells