In order to understand the development of the thymus, both in terms of T cell differentiation and the stromal cell environment, we have undertaken a molecular approach to identify the genes expressed in this tissue. Our strategy is to make two cDNA libraries: one from total thymus of 129 mice, the other from BALB/c mice expressing the SCID mutation. The latter has a developmental arrest at the IL-2 receptor alpha high double negative stage of T cell development; thus, the cDNA library from this mouse will be enriched for genes expressed in early T cell precursors and the stromal cells. We are currently developing several methods to screen these libraries, including subtractive hybridization, massive cDNA sequencing, probing with PCR-based libraries generated from rigorously defined T cell subsets, and differential display. At this early stage of the project, we have prepared the two cDNA libraries from total and SCID thymus. Although we have only just begun some preliminary sequencing, we have already identified the mouse ARF-3 protein (a small GTP binding protein involved in vesicular transport) and a new beta3 integrin (involved in cell adhesion), as well as a third gene with no known homology to anything in the GenBank data base.