This application is to support the distribution to the sea urchin developmental molecular and cell biology research community of high density arrayed filters (macroarrays) containing large cDNA libraries, that represent every stage of embryogenesis, several individual cell types, and various adult tissues. We will also create and distribute microarrays bearing genes of specific interest to the community. Both macro- and microarrays will be generated using the Genetix robot at Caltech. The cDNA libraries have already all been constructed and arrayed as part of the Strongylocentrotus puipurntus Genome Project. Macroarray filter distribution to selected laboratories has been initiated on a pilot scale, with extremely enthusiastic responses, as attested by letters within the Application. Quality control testing will be routinely carried out, and the service we intend to maintain will include recovery and shipping of any clones identified by users of the macroarrays on request. The arrayed libraries wffl be maintained in freezer banks in my laboratory. An important additional objective is the management of a continuously updated, publicly available web site data base in which information as to the identity of clones in the arrays is accumulated from all laboratories utilizing them. The ancillary research and development component of the proposed work includes the perfection of a powerful new methodology for differential subtractive hybridization on the macroarrays; measurement of hybridization kinetics on microarrays to establish useful parameters of sensitivity under diverse experimental situations; development of probes for use on both micro-and macroarrays that represent any given regulatory state in the sea urchin embryo; and completion of a custom made unique processing system for quantitative differential analysis of macroarray screens using complex probes.
| Barsi, Julius C; Tu, Qiang; Calestani, Cristina et al. (2015) Genome-wide assessment of differential effector gene use in embryogenesis. Development 142:3892-901 |
| Tu, Qiang; Cameron, R Andrew; Davidson, Eric H (2014) Quantitative developmental transcriptomes of the sea urchin Strongylocentrotus purpuratus. Dev Biol 385:160-7 |
| Cameron, R Andrew (2014) Tools for sea urchin genomic analysis. Methods Mol Biol 1128:295-310 |
| Tu, Qiang; Cameron, R Andrew; Worley, Kim C et al. (2012) Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis. Genome Res 22:2079-87 |
| Cameron, R Andrew; Samanta, Manoj; Yuan, Autumn et al. (2009) SpBase: the sea urchin genome database and web site. Nucleic Acids Res 37:D750-4 |
| Smith, Joel; Kraemer, Ebba; Liu, Hongdau et al. (2008) A spatially dynamic cohort of regulatory genes in the endomesodermal gene network of the sea urchin embryo. Dev Biol 313:863-75 |
| Andrew Cameron, R; Davidson, Eric H (2007) A basal deuterostome genome viewed as a natural experiment. Gene 406:1-7 |
| Sea Urchin Genome Sequencing Consortium; Sodergren, Erica; Weinstock, George M et al. (2006) The genome of the sea urchin Strongylocentrotus purpuratus. Science 314:941-52 |
| Materna, Stefan C; Berney, Kevin; Cameron, R Andrew (2006) The S. purpuratus genome: a comparative perspective. Dev Biol 300:485-95 |
| Bottjer, David J; Davidson, Eric H; Peterson, Kevin J et al. (2006) Paleogenomics of echinoderms. Science 314:956-60 |
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