Global survey of transcriptome dynamics can provide molecular insights into cell physiology. In the past few years, DNA microarray for transcriptome analysis has been augmented by high-throughput sequencing methods; extending the reach of transcriptome analysis to the rodent species of biotechnological importance, for which the development of genomic tools has been lagging. The rapid accumulation of sequencing data for these species highlighted the need for more evidence-based annotation. Recent findings in the epigenetic regulation in human and mouse will inspire similar research in CHO and BHK cells. Transcriptome studies in these recombinant cells will likely lay the foundation for a systems-based genome engineering which can be used to develop superior producing cell lines. Herein, we summarized the recent findings and advances in transcriptome studies of cell culture bioprocesses. The potential impact of transcriptomics on biopharmaceutical process technology is also discussed.