Cellular and cell-free therapies have provided novel therapeutic opportunities for treating various incurable diseases. This is because the mesenchymal stromal/stem cells (MSCs) produce a plethora of bioactive molecules able to target different biological pathways through extracellular vesicle-mediated paracrine mechanisms simultaneously. However, to share transcriptomic signatures with their origin tissue, it is expected that each MSC population has a unique molecular profiler. In this sense, to analyze the transcriptome of therapeutic cells, it is crucial to identify the molecular profiler of these cells to predict the potential clinical benefits promoted by these cells. Herein, we discuss the application of high-throughput RNA-sequencing (RNA-Seq) in the Pharma Intelligence Era, discussing and exemplifying how the combination of molecular biology with Analytics can revolutionize the Research, Development, & Innovation (RD&I) of advanced medicinal products.