Squamous cell carcinoma or SCC of horn in bovines (bovine horn core carcinoma) frequently observed in Bos indicus affecting almost 1% of cattle population. Freshly isolated primary epithelial cells may be closely related to the malignant epithelial cells of the tumor. Whole transcriptome sequencing of horn’s SCC tissue derived early passage BHCC cells and late passage BHCC cells were done using Ion Torrent PGMR. Comparative expression and analysis of different genes and pathways were observed. Cancer related TGF beta signalling pathway, PI3K/Akt signaling, Ubiquitin mediated proteolysis in early passage BHCC cells and pentose phosphate pathway in late passage BHCC cells were discussed. The cells at later passages could retain the transcriptomic signature of horn cancer.