Abstract: The present invention relates to materials and methods for the quantitative and qualitative analysis of gene expression during targeted differentiation of isolated homozygous stem cells, and to materials and methods for accumulating sequence tags sampled from a population of expressed genes. More particularly, the present invention relates to a method for constructing a model of cellular development and differentiation comprising the steps of: (1) producing a homogenous population of homozygous stem (HS) cells; (2) directing the differentiation of the HS cells to arrive at desired mature (somatic) cells, group of cells or tissue; (3) periodically sampling HS cells undergoing differentiation to extract total cellular RNA produced at various sampling stages; (4) isolating mRNA from the total cellular RNA; and (5) constructing a cDNA library representative of proteins produced and expressed at various stages of differentiation, over the course of time.