Mice were euthanized via CO2 inhalation at 7 days post-infection. Brains were harvested and flash-frozen in a dry ice and methylbutane slurry mix before infection sites were cut using a brain matrix. RNA extraction was done using the Zymo Quick-mRNA kit followed by an in-column DNase treatment. Isolated RNA was eluted in nuclease-free water and stored at -80 The RNA library prep was prepared using the Illumina RNA-Seq libraries Poly A kit with a normalized input of 250 ng per sample.  The RNA library prep was prepared using the Illumina Stranded mRNA Prep kit with a normalized input of 250 ng per sample. Libraries were checked for quality and quantified using the 4200 TapeStation