High-depth transcriptomic profiling reveals the temporal gene signature of human mesenchymal stem cells during chondrogenesis

Mesenchymal stem/stromal cells (MSCs) provide an attractive cell source for cartilage repair and cell therapy; however, the underlying molecular pathways that drive chondrogenesis of these populations of adult stem cells remain poorly understood. We generated a rich data set of high-throughputRNAsequencing of human MSCs throughout chondrogenesis at 6 different time points. Our data consisted of 18 libraries with 3 individual donors as biologic replicates, with each library possessing a sequencing depth of 100 million reads. Computational analyses with differential gene expression, gene ontology, and weighted gene correlation network analysis identified dynamic changes inmultiple biologic pathways and,most importantly, a chondrogenic gene subset,whose functional characterization promises to further harness the potential ofMSCs for cartilage tissue engineering. Furthermore,we created a graphic user interface encyclopedia built with the goal of producing an open resource of transcriptomic regulation for additional dataminingandpathway analysis of theprocess ofMSCchondrogenesis.