This proposal seeks support for the Arrayed Gene Library Resource for the purple sea urchin, Strongylocentrotus purpuratus. This Resource is the sole provider of genomic materials for the whole genome sequencing effort in addition to its service to the cell and developmental research community. There are two parts to the Resource: a robotic arrayed library and a computational facility. The robotics facility generates, maintains and distributes arrayed library materials to the research commuinity. The new service aims are web pages to enhance the usefulness of the system. The pages will detail: 1) perturbing reagents, probes, and specific gene primers used in this system; 2) expression and function of sea urchin transcription factors; 3) links between sea urchin DMA sequences and resource plasmid clones; 4) implement distribution of specific software and documentation; and 5) list community specific information. In the research component we will provide cDNA libraries to inform the annotation of the genome. We plan to: 1) to produce a tissue-specific library from adult radial nerve; 2) to produce a library containing adult skeletogenic genes; 3) to construct a library containing differentiation genes for adult oral structures; 4) to produce a library from the juvenile lantern for muscle genes; and 5) to determine the quality of existing adult tissue libraries We envision the Sea Urchin Genome Resource as part of a distributed system whose individual efforts make up a highly connected, useable whole genome resource. We act as a portal to bring the accumulated experience of experimental developmental biology to bioinformaticists. And we present the bioinformatics tools and databases of genomic sequence collections to the experimentalist. All of the individual goals detailed above are direct responses to this view.
| 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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