Single-cell cDNA microarray profiling of complex biological processes of differentiation

Gene expression profiling at the single-cell level has been used to identify genes expressed in specific cell populations, in attempts to address various fundamental questions in multicellular organisms. In this article, we review the advance of single-cell cDNA amplification techniques in the last decade, and introduce a recently developed, reliable, quantitative method that is applicable to genome-wide transcriptional analyses with high-density oligonucleotide microarray and massively parallel sequencing. This method has been applied to a variety of biological studies, including developments of blastocyst inner cell mass, neurons, and primordial germ cells, to profile the molecular properties, dynamics during differentiation, and impacts of gene alterations in the individual cells in depth. These studies uncovered complex behaviors of the cells during differentiation in vivo, and identified previously unknown, transient populations that emerged in specific stages of development. These achievements clearly demonstrated that it is now more feasible to analyze gene expression in any cell type of interest in a quantitative, genome-wide manner at the single-cell resolution.