Guo, G. et al. Cell Stem Cell 13, 492–505 (2013).

Methods to measure gene expression in single cells are in high demand. Several such methods are currently in use, but higher throughput and coverage are still desirable. Guo et al. now improve reverse transcription–quantitative PCR (RT-qPCR) from single cells, using algorithms for primer design and optimizing experimental conditions to measure up to 280 markers in 1,500 single cells in a multiplex fashion. They implement this approach to quantitatively measure gene expression of selected markers in normal and leukemic mouse hematopoietic stem and progenitor cells as well as in mature blood cell types. They demonstrate that analysis of the resulting data can capture known lineage relationships between cells. This improved approach should enable the study of dynamic and heterogeneous cell populations beyond those in the bone marrow.