Bovine host transcriptomics to evaluate how markets and vaccines influence health and disease
To evaluate how commercially available vaccines and marketing strategy affect the host transcriptome of commercial beef cattle overtime, we sequenced the whole blood RNA of 73 commercial beef bull calves enrolled in a split plot study. Calves were randomized to one of four groups, having received a commercially available vaccine during the cow-calf phase or not, and placed in a commercial salebarn system after weaning (auction) or directly shipped to backgrounding (direct). Samples were acquired from six time points: T1 (modified live viral (MLV) vaccination; age: ~107 d.), T2 (seven days post-vaccination; age: ~114 d.), T3 (revaccination; age: ~183 d.),  T4 (abrupt weaning; age: ~230 d.), T5 (arrival to backgrounding after marketing decision; age: ~233 d.), and T6 (45 days post-arrival to backgrounding; age: ~278 d.). Further evaluation was made based on whether calves were clinically diagnosed with bovine respiratory disease (BRD) after weaning. Overall design: Whole blood from 73 randomly selected individuals with relative equal allocation across study group and disease acqusition were used for gene expression profiling and differential analysis across six time points (T1-T6).