Viral gain-of-function experiments uncover residues under diversifying selection in nature

Rohan Maddamsetti; Daniel T. Johnson; Stephanie J. Spielman; Katherine L. Petrie; Debora S. Marks; Justin R. Meyer

The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/242495 doi: bioRxiv preprint Supplementary Table S1 | Oligonucleotides (oligos) used to edit l genomes. Oligos were designed slightly differently for the two libraries. For the first, we inserted a synonymous change near each target. This was done as a silent tag to improve our confidence that an edit had been made successfully. We did not do this for the second library because we found that all intentional nonsynonymous changes were accompanied by the synonymous change. Additionally, for the first library, when mutations fell within 90 bases, we designed a separate oligo for each possible mutation combination. For the second library, we ordered a mixed pool of oligos synthesized that had all combinations of the mutations. Asterisks indicate phosphorothioated bases.