Systemix Institute

NEW Tiling array data mapped to V2.1 genome assembly.

Purified poly-A RNA mixed in equal quantities from egg, early blastula, gastrula and prism stage embryos was hybridized on 27 high-density arrays containing 50-mer probes chosen from the entire sea-urchin genome. Array experiments were conducted at Dr. Viktor Stolc's lab at NASA Ames Genome Research Facility. RNA samples were provided by Prof. Eric Davidson's lab at Caltech. Each array contained 400,000 unique features and was synthesized using a maskless array synthesizer technology. More details on the design of the array experiment and what the images shown below mean can be found from here.

Raw data for our experiment is available from the NCBI GEO database (GSE6031).

If you find our data useful, please cite: Manoj Pratim Samanta, Waraporn Tongprasit, Qiang Tu, Sorin Istrail, Andy Cameron, Eric H. Davidson, Viktor Stolc, Science, Science. 2006 314(5801):960-2.

(a) Check signals for few well-annotated genes here

Here is a description of the X and Y-axes, and experimental procedure.

(b) View by Glean ID

(c) Plot by location

CITATIONS
During the course of sea urchin genome project, tiling data was used extensively to annotate genes of different functional categories. Results from these excellent research activities are reported in the following manuscripts.

Embryonic Expression Profile (time-course measurement): Wei, Z., Angerer, R.C., Angerer, L.M. Developmental Biology (2006). here

Signaling genes (protein phosphatases): Byrum, C.A., Walton, K.D., Robertson, A.J., Corbonneau, S., Thomason, R.T., Coffman, J.A., and McClay, D.R., Developmental Biology (2006). here

Neural genes R.D. Burke, L.M. Angerer, M.R. Elphick, G.W. Humphrey, S. Yaguchi, T. Kiyama, S. Liang, X. Mu, C. Agca, W.H. Klein et al. Developmental Biology (2006). here

Signaling genes (RTK and TGF-beta) Francois Lapraz, Eric Rottinger, Veronique Duboc, Ryan Range, Louise Duloquin, Katherine Walton, Shu-Yu Wu, Cynthia Bradham, Mariano A. Loza, Taku Hibino et al. Developmental Biology (2006). here

Signaling genes (Notch and hedgehog) Walton, Katherine D., Croce, Jenifer C., Glenn, Thomas D., Wu, Shu-Yu, McClay, David R. Developmental Biology (2006). here

Chemical defensome J. V. Goldstone, A. Hamdoun, B.J. Cole, M. Howard-Ashby, D. Nebert, M. Scally, M. Dean, D. Epel, M.E. Hahn and J.J. Stegeman, Developmental Biology (2006). here

Wnt signaling pathway Croce, J. C., Wu, S., Byrum, C., Xu, R., Duloquin, L., Wikramanayake, A. H., Gache, C., McClay, D. R. Developmental Biology (2006). here

Adhesome Charles A. Whittaker, Karl-Frederik Bergeron, James Whittle, Bruce P. Brandhorst, Robert D. Burke and Richard O. Hynes Developmental Biology (2006). here

Oogenesis Jia L. Song, Julian L. Wong and Gary M. Wessel, Developmental Biology (2006). here

Apoptosis Anthony J. Robertson, Jenifer Croce, Seth Carbonneau, Ekaterina Voronina, Esther Miranda, David R. McClay and James A. Coffman, Developmental Biology (2006). here

Zinc finger Stefan C. Materna, Meredith Howard-Ashby, Rachel F. Gray and Eric H. Davidson Developmental Biology (2006). here

G-protein coupled receptors Florian Raible, Kristin Tessmar-Raible, Enrique Arboleda, Tobias Kaller, Peer Bork, Detlev Arendt, and Maria I. Arnone, Developmental Biology (2006). here

GTPases Wendy S. Beane, Ekaterina Voronina, Gary M. Wessel, and David R. McClay. Developmental Biology (2006). here

Cell cycle Antonio Fernandez-Guerra, Antoine Aze, Julia Morales, Odile Mulner-Lorillon, Bertrand Cosson, Patrick Cormier, Cynthia Bradham, Nikki Adams, Anthony J. Robertson, William F. Marzluff et al. Developmental Biology (2006). here

Forkhead transcription factors Qiang Tu, C. Titus Brown, Eric H. Davidson, Paola Oliveri Developmental Biology (2006). here

Kinome Bradham C, Foltz KR, Beane WS, Arnone Mi, Rizzo F, Coffman JA, Mushegian A, Goel M, Morales J, Geneviere AM, Lapraz F, Robertson AJ, Kelkar H, Loza-Coll M, Townley IK, Raisch M, Roux MM, Lepage T, Gache C, McClay DR, and G Manning. Developmental Biology (2006). here

Metalloprotease Lynne Angerer, Sofia Hussain, Zheng Wei and Brian T. Livingston Developmental Biology (2006). here