Expression profiling of mouse embryonic stem cells by mass spectrometry

Embryonic stem cells from B6 and NOD backgrounds were derived freshly in the presence of 2i. After 3-5 passages on feeders, ES cells were cultured in 2i media without any feeders for several passages. In order to identify differentially expressed genes and proteins, we performed RNA-Seq and mass spectromety analysis respectively. Among the differentially expressed genes, we identified several important players in innate and adaptive immunity. Several of these genes had been linked to onset of type-1 diabetes. Proteomics analysis was able to quantitative differences in protein expression among the B6 and NOD ES cell lines.