|
| 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
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| 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.
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| Web link |
http://www.systemix.org/sea-urchin
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| |
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| 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 |
| E-mail(s) |
manoj.samanta@systemix.org
|
| 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) |
| GPL4428 |
sea urchin tiling array urchin4 (BC459) |
| GPL4429 |
sea urchin tiling array urchin5 (BC455) |
| GPL4430 |
sea urchin tiling array urchin6 (BC458) |
| GPL4431 |
sea urchin tiling array urchin7 (BC460) |
| GPL4432 |
sea urchin tiling array urchin8 (BC461) |
| GPL4433 |
sea urchin tiling array urchin9 (BC446) |
| GPL4434 |
sea urchin tiling array urchin10 (BC448) |
| GPL4435 |
sea urchin tiling array urchin11 (BC452) |
| GPL4436 |
sea urchin tiling array urchin12 (BC451) |
| GPL4437 |
sea urchin tiling array urchin13 (BC468) |
| GPL4438 |
sea urchin tiling array urchin14 (BC465) |
| GPL4439 |
sea urchin tiling array urchin15 (BC463) |
| GPL4440 |
sea urchin tiling array urchin16 (BC462) |
| GPL4441 |
sea urchin tiling array urchin17 (BC444) |
| GPL4442 |
sea urchin tiling array urchin18 (BC445) |
| GPL4443 |
sea urchin tiling array urchin19 (BC466) |
| GPL4444 |
sea urchin tiling array urchin20 (BC454) |
| GPL4445 |
sea urchin tiling array urchin21 (BC467) |
| GPL4446 |
sea urchin tiling array urchin22 (BC450) |
| GPL4447 |
sea urchin tiling array urchin23 (BC447) |
| GPL4448 |
sea urchin tiling array urchin24 (BC453) |
| GPL4449 |
sea urchin tiling array urchin25 (BC449) |
| GPL4450 |
sea urchin tiling array urchin26 (BC443) |
| GPL4451 |
sea urchin tiling array urchin27 (BC464) |
|
| Samples (27)
|
| GSM140013 |
sea urchin tiling array urchin1 (BC456) |
| GSM140014 |
sea urchin tiling array urchin2 (BC442) |
| GSM140015 |
sea urchin tiling array urchin3 (BC457) |
| GSM140016 |
sea urchin tiling array urchin4 (BC459) |
| GSM140017 |
sea urchin tiling array urchin5 (BC455) |
| GSM140018 |
sea urchin tiling array urchin6 (BC458) |
| GSM140019 |
sea urchin tiling array urchin7 (BC460) |
| GSM140020 |
sea urchin tiling array urchin8 (BC461) |
| GSM140021 |
sea urchin tiling array urchin9 (BC446) |
| GSM140022 |
sea urchin tiling array urchin10 (BC448) |
| GSM140023 |
sea urchin tiling array urchin11 (BC452) |
| GSM140024 |
sea urchin tiling array urchin12 (BC451) |
| GSM140025 |
sea urchin tiling array urchin13 (BC468) |
| GSM140026 |
sea urchin tiling array urchin14 (BC465) |
| GSM140027 |
sea urchin tiling array urchin15 (BC463) |
| GSM140028 |
sea urchin tiling array urchin16 (BC462) |
| GSM140029 |
sea urchin tiling array urchin17 (BC444) |
| GSM140030 |
sea urchin tiling array urchin18 (BC445) |
| GSM140031 |
sea urchin tiling array urchin19 (BC466) |
| GSM140032 |
sea urchin tiling array urchin20 (BC454) |
| GSM140033 |
sea urchin tiling array urchin21 (BC467) |
| GSM140034 |
sea urchin tiling array urchin22 (BC450) |
| GSM140035 |
sea urchin tiling array urchin23 (BC447) |
| GSM140036 |
sea urchin tiling array urchin24 (BC453) |
| GSM140037 |
sea urchin tiling array urchin25 (BC449) |
| GSM140038 |
sea urchin tiling array urchin26 (BC443) |
| GSM140039 |
sea urchin tiling array urchin27 (BC464) |
|
| Relations |
| BioProject |
PRJNA97757 |
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