Small RNA sequencing and RNA sequencing of VACV-infected cells

Quality control and adapter trimming were performed using Trim Galore (v0.6.4) with default parameters, and reads length between 17 and 70 were used for subsequent analyses. The sequenced reads were mapped to the human genome (release hg19) by using Bowite2 2.3.5.  Libraries of RNAs from RNA-IP samples were constructed using MGIEasy RNA Library Preparation Kits (BGI) according to manufacturer’s protocols, and then sequenced by MGISEQ2000 (BGI) at Wuhan Institute of Virology, CAS.

Quality control and adapter trimming were performed using Trim Galore (v0.6.4) with default parameters. All clean reads were aligned to the viral genome using STAR (v2.7.11b) with strand-specific quantification, allowing separate abundance estimation for the (+)- and (-)-stranded genomes.