Assays

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 ...