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Series GSE6031 Query DataSets for GSE6031
Status Public on Oct 23, 2006
Title A high-resolution transcriptome map of the sea urchin embryo
Organism Strongylocentrotus purpuratus
Experiment type Expression profiling by genome tiling array
Summary The sea urchin S. purpuratus is a model organism for study of the genomic control circuitry underlying embryonic development. We examined the complete repertoire of genes expressed in the S. purpuratus embryo, up to late gastrula stage, by means of high-resolution custom tiling arrays covering the whole genome. We detected complete spliced structures even for genes known to be expressed at low leveles in only a few cells. At least 11,000 to 12,000 genes are used in embryogenesis. These include most of the genes encoding transcription factors and signaling proteins, as well as some classes of general cytoskeletal and metabolic proteins, but only a minor fraction of genes encoding immune functions and sensory receptors. Thousands of small asymmetric transcripts of unknown function were also detected in intergenic regions throughout the genome. The tiling array data were used to correct and authenticate several thousand gene models during the genome annotation process.

Keywords: high-resolution tiling array, sea urchin, embryo
Keywords: other
Overall design Poly-A RNA from egg, early blastula (15hr.), early gastrula (30hr.) and late gastrula stage (45hr.) embryos of sea urchin were mixed in equal quantities. The RNA sample was converted to cDNA and fluorescently labeled. Single hybridization experiment was performed.
Web link
Contributor(s) Samanta MP, Tongprasit W, Istrail S, Cameron RA, Tu Q, Davidson EH, Stolc V
Citation(s) 17095694
Submission date Oct 13, 2006
Last update date Mar 16, 2012
Contact name Manoj Samanta
Phone 408-472-7927
Organization name Systemix Institute
Street address 2240 Homestead Court #309
City Los Altos
State/province CA
ZIP/Postal code 94024
Country USA
Platforms (27)
GPL4425 sea urchin tiling array urchin1 (BC456)
GPL4426 sea urchin tiling array urchin2 (BC442)
GPL4427 sea urchin tiling array urchin3 (BC457)
Samples (27)
GSM140013 sea urchin tiling array urchin1 (BC456)
GSM140014 sea urchin tiling array urchin2 (BC442)
GSM140015 sea urchin tiling array urchin3 (BC457)
BioProject PRJNA97757

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