Solid phase selection of differentially expressed genes

The present invention provides a method and materials for examining and isolating differentially expressed genes. In the method of the present invention, different labeled populations of DNAs from sources to be compared are competitively hybridized with reference DNA cloned on solid phase supports, e.g. microparticles, to provide a differentiated expression library as the preferred embodiments, can be manipulated by fluorescence-activated cell sorting (FACS). Examination of the relative signal intensity of different fluorescence labels on the microparticles enables quantitative analysis of expression levels relative to reference DNA. The invention also provides a method for identifying rare gene isolates. Populations of microparticles having relative signal intensities of interest can be isolated by FACS and the bound DNAs identified by sequencing, such as by large-scale parallel signature sequencing (MPSS), or by standard DNA sequencing methods.