“Not just the FACS, ma’am, not just the FACS.” These words could have come from investigators who have applied a new technique to assess gene expression in stem cells. FACS, or fluorescence-activated cell sorting, is used to remove cells from their native environment and purify them for analysis. Another, newer technique, however, may better reflect stem cells’ in vivo state.

The new technique, which labels newly transcribed RNA in vivo , has been applied by scientists based at Stanford University School of Medicine. According to these scientists, the in vivo approach reveals transcriptional nuances that cannot be captured by FACS, whether this isolation procedure is combined with ordinary culture techniques, or specialized techniques that temporarily arrest transcription.

The Stanford team, led by Thomas Rando, M.D., Ph.D., professor of neurology and neurological sciences, focused on muscle stem cells (MuSCs) in mice. When snug in the body, MuSCs tend …