Enrichment of RNase H cleavage products by size and affinity selection. The RNase H cleavage product (input) was first size-selected by two rounds of NEBNext magnetic beads. The clarified unbound fraction of the second round of size selection (ub2) was then added directly to streptavidin magnetic beads for affinity selection. After the first wash using a standard wash solution containing 1 M NaCl (W1), the resuspended bead slurry was divided into two fractions. One fraction was washed three more times using the standard wash buffer (W4_HS) and eluted using biotin (Eluate_biotin). The other fraction of the slurry was washed three more times using a low NaCl wash solution (W4_LS) followed by elution using the same volume of water (Eluate_water). Similar amounts of RNase H cleavage product and TO were eluted (also see Supplemental Fig. 4).
