Latest Echinobase Content
Visit the previous echinobase.org
Gene nomenclature and related ID questions.
Echinobase has data available for download through the FTP site with a tutorial video.
Anneissia japonica (feather star)
Echinoderms are model organisms for studying embryo development and regeneration due to many unique features including:
- the ability to synchronize fertilization of millions of eggs
- transparent embryos and larvae
- varied development within and between a genus
Echinobase is organized around the genepage which collects and displays information about genes, orthology, and links to research papers and gene models of echinoderm species are associated with the genome sequence using JBrowse. Temporal developmental gene expression data will be displayed when available, and spatial cell type information will be associated using the Echinoderm Anatomical Ontology (ECAO).
Echinobase provides a critical data sharing infrastructure for other NIH-funded projects, and is a focal point for the echinoderm community. In addition to our primary goal of supporting echinoderm researchers, Echinobase enhances the availability and visibility of Echinoderm data to the broader biomedical research community.
The substantially improved current release of the purple sea urchin genome assembly (Spur5.0) is sixth in the series.
The development of echinoderm embryos and larvae has been studied for over 100 years. Echinoderm eggs are fertilized externally and embryos and larvae are transparent, enabling detailed descriptions of the structure and timing of the development of multiple species. The variation in developmental patterns is used to improve understanding of these vital processes in echinoderms and deuterostomes.
Skeletogenesis in echinoderms is diverse and well documented and an area of active research.
Regeneration capability makes echinoderms ideal organisms for the study of these processes at the anatomical and genetic levels.
Animal suppliers and protocolsProtocols and reagents for studying gene expression:
Microinjection, morpholinos and BACsGenomics methods:
RNA-seq and scRNA-seq
ChIP-seq and ATAC-seq
The Echinoderm Community is able to submit new genomes for partial support when assembly and annotation are publicly available through Genbank. The assemblies, annotations, and functional data tracks (GFF files) will be available on JBrowse and can be searched via BLAST.
The Echinobase PIs and SAB members will decide the new species for full support and integration into the database as gene pages with complete functionality, including gene names and symbols, synonyms, literature, orthology, and developmental gene expression display. This process will only be possible when the genome has been fully processed by the NCBI annotation pipeline. Suggestions for priority species are always welcome.