Single-cell cDNA high-density oligonucleotide microarray analysis: detection of individual cell types and properties in complex biological processes

Gene expression analyses at the single-cell level have been identifying genes that are expressed and play key roles in distinct populations of cells constituting a wide variety of tissues in multicellular organisms. With the development of high-density oligonucleotide microarray platforms covering whole genome transcript information from many organisms, the demand has grown for methods of quantitative global mRNA amplification from a small number of cells, especially single cells. This article reviews briefly some of the pioneering studies in the detection of genes expressed in single cells of interest, with emphasis on the quantitative performance of the amplification methodologies employed. Based on these studies, a highly quantitative global single-cell cDNA amplification procedure has recently been developed that is immediately applicable to high-density oligonucleotide microarray analysis. Indeed, the method has revealed that the inner cell mass cells of mouse early blastocysts show distinctive gene expression indicative of their differentiation towards either primitive endoderm or pluripotent epiblast as early as embryonic day 3.5, 1 day before these cells are morphologically distinguishable. Thus, it has now become more practical to uncover the genome-wide expression properties of any given cell type in desired biological contexts at single-cell resolution, creating unprecedented analytical opportunities in the biomedical sciences.