This pathology is likely a result of many complex factors, as there is increasing evidence that the host response to viral infection is one of the main causes of pathology and survival during WNV infection in the CNS. In humans and horses, long term recovery responses are variable, with evidence of moderate to severe congnitive, emotional, and motor deficits in humans, and behavioral and motor deficits in horses. Thus there is a gap in our understanding of the interactions between various components of the natural host response to infection, and how these interactions can lead to pathology, long term deficits, or full recovery. Given the similarities between disease in horses and humans, equine tissue analysis offers an unparalleled opportunity to profile gene expression and pathway interactions between pathogens and the CNS. Although there are many new methods for profiling gene expression, there is limited development of de novo deep sequencing strategies due to limited financial resources and species specific bioinformatics in veterinary research fields. In terms of adaptability and computational resources, microarrays allow rapid acquisition of tissue specific expression data for many non-model species. Microarrays have facilitated the study of the Flaviviridae in multiple applications including detection of variants of Dengue virus in human samples, differentiation between different flaviviral and other viral infections, and mutations in the structural regions of the WNV genome. Microarrays have been used to analyze gene expression at both the cell culture and organism level for DV, JEV, and yellow fever virus infection. Although several species specific arrays exist, there is limited development of tissue specific arrays in veterinary medicine. The microarray currently developed in the horse is based on global gene expression in which multiple tissues of the equine transcriptome were sequenced. While a valuable tool, only cerebrum, cerebellum and spinal cord were utilized in this work to generate transcriptome data. Two studies have used microarrays to examine gene expression changes in response to WNV infection. In one, human Salvianolic-acid-B glioblastoma cell culture transcriptional responses to WNV were analyzed, and 23 genes involved in neurodegenerative disorders were shown to be Apoptosis Activator 2 changed in expression. In the other, a microarray was used to analyze whole organism gene expression response to WNV strains of different neurovirulence in a mouse model. Genes involved in immunological, neurological, and apoptotic functions were differentially regulated. No studies are available that profile gene expression in the CNS of animals infected with WNV that are considered natural, susceptible hosts. These data could provide detailed information on the host response to infection and on a pathogen��s specific manipulation of the host response, and will also allow more efficient analysis of essential pathways in model species such as mouse and hamster. This report provides sequencing data from the equine brain transcriptome and lymphoid system from naive horses experimentally infected with WNV, vaccinated horses experimentally infected with WNV, and negative controls. Also described is the construction of a custom, validated equine high density microarray, in which pathways of the CNS and immune system were enriched. The microarray was used to profile gene expression changes in the thalamus and cerebrum of naive and vaccinated horses during experimental WNV infection and common gene pathways were identified.