Identification of differentially expressed genes in the visual structures of brain using high-density cDNA grids

The hybridization patterns of 18,371 high-density-grid-arrayed non-redundan t complementary DNA (cDNA) clones were examined using three different sourc es of cDNA probes. The first set of probes was synthesized from mRNA isolat ed from visual brain areas MT and V4 of Vervet monkey. The second set of pr obes was derived from cDNA libraries constructed from two micro dissected s ets of layers of the monkey Lateral Geniculate Nucleus layers within the vi sual pathway, namely the magnocellular and parvocellular layers. The third set of cDNA probes was synthesized from the subtracted fractions of the cDN As enriched for either the magnocellular or the parvocellular layers of the Lateral Geniculate Nucleus. Software, linked directly to the Genbank datab ase, was developed to aid in the rapid identification of bath expressed and differentially expressed genes. Our results indicate that both the cDNA pr obes synthesized from mRNA and cDNA libraries can identify similar fraction s of expressed genes. However, the subtracted cDNA probes improve the effic iency of detection for those genes that are expressed at much lower abundan ce. Analyses of these results for the differential expression patterns of t hese genes were validated by semi-quantitative PCR on the DNA derived from the whole tissue cDNA libraries. A list of some known genes that are statis tically differentially expressed within the magnacellular layers of the LGN and area MT in the primate visual areas is derived. (C) 2000 Elsevier Scie nce B.V. All rights reserved.