RIP-seq of Ebola virus VP40  bound RNA
In order to assay RNA features of all sizes, we adapted the NEXTFLEX Small RNA-Seq Kit protocol (PerkinElmer). Specifically, RNA was sheared naturally during the cell lysis and Strep-Tactin bead incubation stages described above (Figure S5A); and in order to include RNA fragments up to ~300 nucleotides, we omitted the upper-bound bead purification from protocol step F. Multiplexed libraries were sequenced using a version 3 paired-end 150-cycle MiSeq flow cell (Illumina).