Table 1.

Initial training datasets identified for ML testing. A total of 160 mRNA-Seq datasets were derived from lymph node and lung tissue of 31 cattle challenged with isolated BRD pathogens and 10 sham challenged controls. Asterisk (*) indicates different tissues collected from the same animals. Specifically, transcriptomes from tissues reported by Behura et al.³¹ are from the same cattle from which Tizioto et al. analyzed bronchial lymph node transcriptomes (2015) except that P. multocida infected cattle reported by Tizioto et al.³⁰ are not included in the cohort reported by Behura et al.³¹.

NCBI BioProject ID	Animal breed	Animal age	Number of animals	Tissue types	Etiological agents used in challenge	Sequencing platform	Publication
PRJNA272725	Angus × Hereford (steers)	6–8 mon	n = 23 challenge; n = 4 control	Bronchial lymph node	BRSV* (n = 4), BVDV* (n = 4), IBR* (n = 4), M. haemolytica* (n = 4), P. multocida* (n = 4), M. bovis* (n = 3), control* (n = 4)	Illumina HiSeq 2500; 50 bp PE	Tizioto et al., 2015 (n = 27)
PRJNA272725	Angus × Hereford (steers)	6–8 mon	n = 19 challenge; n = 4 control	Lung (healthy), lung (lesion), retropharyngeal lymph node, nasopharyngeal lymph node, pharyngeal tonsil	BRSV* (n = 4), BVDV* (n = 4), IBR* (n = 4), M. haemolytica* (n = 4), M. bovis* (n = 3), control* (n = 4)	Illumina HiSeq 2500; 50 bp PE	Behura et al., 2017 (n = 115)
PRJNA543752	Holstein–Friesian (bulls)	~ 4 mon	n = 12 challenge; n = 6 control	Bronchial lymph node	BRSV (n = 12), control (n = 6)	Illumina NextSeq 500; 75 bp PE	Johnston et al., 2019 (n = 18)