A central paradigm of biomedical research is that understanding gene function will ultimately lead to improvements in human health. A crucial first step is to know where and when genes are expressed during embryogenesis and in the adult. The chicken embryo provides many advantages for large-scale expression screening, including striking similarities to human, low expense, and a long history as an experimental model organism. The goal of this renewal application is to continue support and expansion of the GEISHA (gallus expression in situ hybridization analysis) gene expression database, an established community resource for chicken embryo in situ hybridization gene expression information and associated genomic metadata.
Specific aims of this application are (1) to populate the GEISHA database with chicken gene expression information arising from targeted high throughput in situ hybridization screens, from the scientific literature, and from other researchers. High throughput in situ hybridization analyses will be performed to determine the expression patterns of developmental regulatory genes. In situ hybridization images and associated information will also be curated from publications and obtained from researchers. 2) The GEISHA database will be expanded to encompass new types of information and features. In situ hybridization images and associated data will be exchanged with other gene expression projects to enable cross-species display of expression information locally on each platform. The BioMart data integration system and a publication management system will also be added to enhance search and retrieval capabilities and to display gene related publications. 3) The user interface will be enhanced to accommodate new features and to facilitate navigation. Gene Expression Report pages will be reorganized and expanded to include detailed gene summary information, gene-related publications, and gene expression information for multiple species. User-friendly query features will be expanded to include searching by OMIM human disease gene and Gene Ontology terms. Through these enhancements, GEISHA will continue to provide a valuable and comprehensive resource for biomedical research.

Public Health Relevance

The objective of this project is to enhance an important existing gene expression resource for the chicken embryo, a recognized biomedical model of human disease. These services will provide valuable information that will assist efforts across a wide variety of related fields towards the identification of mechanisms underlying human diseases.

National Institute of Health (NIH)
Biotechnology Resource Grants (P41)
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Special Emphasis Panel (ZHD1)
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Coulombe, James N
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University of Arizona
Anatomy/Cell Biology
Schools of Medicine
United States
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Darnell, Diana K; Zhang, Li S; Hannenhalli, Sridhar et al. (2014) Developmental expression of chicken FOXN1 and putative target genes during feather development. Int J Dev Biol 58:57-64
Antin, Parker B; Yatskievych, Tatiana A; Davey, Sean et al. (2014) GEISHA: an evolving gene expression resource for the chicken embryo. Nucleic Acids Res 42:D933-7
Cooley, James R; Yatskievych, Tatiana A; Antin, Parker B (2014) Embryonic expression of the transforming growth factor beta ligand and receptor genes in chicken. Dev Dyn 243:497-508
Darnell, Diana K; Antin, Parker B (2014) LNA-based in situ hybridization detection of mRNAs in embryos. Methods Mol Biol 1211:69-76
Lencinas, Alejandro; Chhun, Danny C; Dan, Kelvin P et al. (2013) Olfactomedin-1 activity identifies a cell invasion checkpoint during epithelial-mesenchymal transition in the chick embryonic heart. Dis Model Mech 6:632-42