The measurement of specific proteins and transcripts in individual cells is critical for understanding the role of cellular diversity in development, health, and disease. Flow cytometry has become a standard technology for high-throughput detection of protein markers on single cells and has been widely adopted in basic research and clinical diagnostics. In contrast, nucleic acid measurements such as mRNA expression are typically conducted on bulk samples, obscuring the contributions from individual cells. Ideally, in order to characterize the complexity of cellular systems, it is desirable to have an affordable approach to examine the expression of a large number of genes across many thousands of cells.