Assays

ZIKV RNA was extracted from virus working stocks using the QIAmp viral RNA minikit (Qiagen, Hilden, Germany). Isolated RNA was then digested with DNase I and purified using the Qiagen RNeasy kit. RNA quality was analyzed on the 2100 bioanalyzer (Agilent, Santa Clara, CA, USA) using the Agilent RNA 6000 Pico assay and quantified on a Qubit fluorometer (Invitrogen, Carlsbad, CA, USA) prior to rRNA depletion and RNA library prep using the KAPA HyperPrep kit (Roche Diagnostics Corporation, Indianapolis, ...

Raw reads were assessed for technical quality control flags using the nSolver software (NanoString) and transferred into RStudio (Boston, MA, USA). As the design of our probe set was nonrandom, we utilized a custom approach for data analysis as previously described to account for large differences in the number of observed counts between mock-infected and infected samples (114). Briefly, we used count data within each sample vector as an internal reference, against which we compared genes of ...