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The Power of Simplicity: Sea Urchin Embryos as in Vivo Developmental Models for Studying Complex Cell-to-cell Signaling Network Interactions
Published on: February 16, 2017
SpBase: the sea urchin genome database and web site.
R Andrew Cameron1, Manoj Samanta, Autumn Yuan
1Center for Computational Regulatory Genomics, Beckman Institute 139-74, California Institute of Technology, Pasadena, CA 91104, USA. acameron@caltech.edu
Nucleic Acids Research
|November 18, 2008
Summary
SpBase provides a public web resource for sea urchin and echinoderm genomic data. This system supports research in cell and developmental biology with genomic sequences and gene annotations.
Area of Science:
- Marine Biology
- Genomics
- Developmental Biology
Background:
- Sea urchins are valuable models for cell and developmental biology research.
- Genomic information is crucial for understanding echinoderm evolution and biology.
Purpose of the Study:
- To provide an accessible, user-friendly database of genomic information for sea urchins and related echinoderms.
- To support experimental work in cell and developmental biology using these research models.
Main Methods:
- Development and maintenance of a public web-based database system (SpBase).
- Integration of genomic sequence data, expressed sequences, and gene annotations.
- Implementation of search functionalities for sequences and gene annotations.
Main Results:
- SpBase offers genomic data for the purple sea urchin (Strongylocentrotus purpuratus) and other echinoderms spanning 540 million years.
- The system includes two purple sea urchin genome assemblies, associated expressed sequences, and gene annotations.
- A database of sequenced clones is also provided, linked to the Sea Urchin Genome resource.
Conclusions:
- SpBase serves as a vital resource for researchers studying echinoderm genomics and biology.
- The database facilitates comparative genomics and evolutionary studies within the echinoderm clade.
- Easy access to comprehensive genomic data enhances the utility of sea urchins as research models.
