Neurons under T cell attack orchestrate phagocyte-mediated synaptic stripping

RNA-seq libraries purified from rLCMV-Cre infected neurons using the Ribotag allele. Seq libraries are provided from STAT1 competent (Stat1+/+ x Rpl22HA/+) or STAT1-deficient (Stat1fl/fl x Rpl22HA/+) rLCMV-Cre carrier mice which have been challenged intravenously with LCMVwt at 5 weeks of age and then sacrificed after 9 days. These seq libraries represent the response of rLCMV-Cre infected neurons to CD8+ T cell attack following challenge with LCMVwt. To investigate how neuronal JAK/STAT1 signaling results in synaptic alterations, we profiled the neuronal translatome by exploiting RiboTag mice (Rpl22HA/+). Upon Cre-mediated recombination of their gene-targeted locus, Rpl22HA/+ mice express an HA-tagged ribosomal protein L22, enabling the immunoprecipitation of ribosome-bound RNA. We inoculated neonatal Rpl22HA/+ mice with rLCMV-Cre, inducing HA-tagged ribosomal expression in infected neurons. Mice were sacrificed 9 days after challenge with LCMVwt in order to extract ribosome-bound mRNA from the brains and perform next generation RNA sequencing. We compared the neuronal translatome of intravenously (i.v) LCMVwt. challenged STAT1-competent (Rpl22HA/+xStat1+/+), conditionally STAT1-deficient (Rpl22HA/+xStat1fl/fl) and non-challenged (Rpl22HA/+ xStat1+/+) rLCMV-Cre carrier mice, respectively. Independent biological replicates (n= 4-7) were analyzed for each group.