In cell LIGR-seq
We performed LIGR-seq in cells infected with the influenza virus. To concentrate viral RNAs in cells, we performed pull-down of viral RNAs by biotinylated antisense ssDNA. 87mut virus has mutations in segment 5 to disrupt the secondary RNA structure of the region. 87rec virus has additional mutations in segment 5 to reconstitute the secondary structure. We set ligation(-) control to negative control samples.