Longitudinal transcriptome analysis of high risk cattle to determine host expressional changes associated with BRD development

Whole blood samples from 36 cattle, across two independent populations, were sequenced via a Illumina NovaSeq 6000 system. Samples were bioinformatically processed in a HISAT2/StringTie pipeline, and stratified based on treatment frequency for BRD (healthy, treated once, treated twice or more and/or died). Differential expression analysis was conducted in R, utilizing an additive, multifactor generalized linear model and blocking for paired samples and year. Genes were considered differentially expressed with an FDR cutoff of 0.10. The objective of this study was to identify differentially expressed genes and mechanisms within and across treatment cohorts overtime, and determine host expressional changes influenced by BRD within the first 28 days of facility arrival. Overall design: 73 whole blood mRNA samples from 36 individual cattle, taken at days 0, 28, and end of study (~63).