Most biological studies are done on populations of cells which may be morphologically and genetically identical but are actually heterogeneous, made up of individual cells with unique expression profi les. Thus,the measurements of nucleic acid and protein levels are an average representation of the pool of individual cells. Single cell analysis allows the study of cell-to cell variation within a cell population (organ, tissue, cell culture). In addition, in-depth analysis of stem cell differentiation and cancer can only be accomplished with single cell analysis. Isolation of single cells is typically accomplished using FACS, microaspiration methods, or laser-capture microdissection. And,because of its sensitivity and dynamic range, RT-qPCR is typically used for expression analysis. Current protocols, however, are limited to interrogating only one analyte type (DNA, RNA or protein) at a time due to limited sample amount and different assay conditions.