The Comparative Functional Genomics Core will support COBRE Project Leaders by providing essential data management and analysis services, and developing a new web-based resource that integrates gene function data from COBRE projects with published studies in several diverse models of regeneration and stem cell self-renewal. Projects utilize high-throughput sequencing technologies and the Core will provide specialized expertise to Project Leaders to effectively manage, analyze and interpret results. Highly experienced Core staff will provide analysis services in a collaborative fashion and feature analysis workflows that will be updated on an ongoing basis. Services include an innovative tool for the analysis of known and novel microRNAs, termed miRMiner, that Core staff developed with a collaborator. The Core will also leverage regional cyberinfrastructure to remotely run large computations on two large clusters and use a regional data center for backup data storage and exchange. In addition to these services, the Core will also construct a new database resource for Project Leaders that has the long-term goal of providing a systems level view of regenerative biology and stem cell self-renewal. The Comparative Models of Regeneration Database (RegenDB) will integrate COBRE gene function data with published studies selected by Project Leaders from a number of comparative models. Initially, RegenDB will feature RNA and miRNA expression data from zebrafish, AxolotI, Xenopus, Polypterus senegalus and mouse embryonic and induced pluripotent stem cells. Project Leaders will be able to quickly compare expression levels of candidate genes within and across experiments they choose using a web interface. Core staff are key participants in the Comparative Toxicogenomics Database that started as an MDIBL pilot project and has since grown into an international resource. The Core will apply this experience to develop RegenDB in a similar fashion and plan to make a public web interface that the scientific community can use to access published data. In summary, the Core provides complementary expertise in bioinformatic analysis and software engineering that Project Leaders need to accomplish their research goals.

Public Health Relevance

The Comparative Functional Genomics Core provides critical data management and analysis for COBRE Project Leaders and establishes a novel informatics resource to conduct a systems-level analysis of regeneration and stem cell self-renewal. The innovative Comparative Models of Regeneration Database will greatly enhance the research efforts of both COBRE Project Leaders and the world-wide scientific community. This in turn will speed the discovery of new regenerative medicine therapies.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Exploratory Grants (P20)
Project #
1P20GM104318-01
Application #
8465635
Study Section
Special Emphasis Panel (ZGM1-TWD-B (CB))
Project Start
Project End
Budget Start
2013-09-01
Budget End
2014-05-31
Support Year
1
Fiscal Year
2013
Total Cost
$398,801
Indirect Cost
$134,101
Name
Mount Desert Island Biological Lab
Department
Type
DUNS #
077470003
City
Salsbury Cove
State
ME
Country
United States
Zip Code
04672
Wu, Cheng-Wei; Deonarine, Andrew; Przybysz, Aaron et al. (2016) The Skp1 Homologs SKR-1/2 Are Required for the Caenorhabditis elegans SKN-1 Antioxidant/Detoxification Response Independently of p38 MAPK. PLoS Genet 12:e1006361
Soundararajan, Ramani; Stearns, Timothy M; Czachor, Alexander et al. (2016) Global gene profiling of aging lungs in Atp8b1 mutant mice. Aging (Albany NY) 8:2232-2252
Lisse, Thomas S; Middleton, Leah J; Pellegrini, Adriana D et al. (2016) Paclitaxel-induced epithelial damage and ectopic MMP-13 expression promotes neurotoxicity in zebrafish. Proc Natl Acad Sci U S A 113:E2189-98
Rizzo, Francesca; Coffman, James A; Arnone, Maria Ina (2016) An Elk transcription factor is required for Runx-dependent survival signaling in the sea urchin embryo. Dev Biol 416:173-86
King, Benjamin L; Yin, Viravuth P (2016) A Conserved MicroRNA Regulatory Circuit Is Differentially Controlled during Limb/Appendage Regeneration. PLoS One 11:e0157106
Davis, Allan Peter; Grondin, Cynthia J; Johnson, Robin J et al. (2016) The Comparative Toxicogenomics Database: update 2017. Nucleic Acids Res :
King, Benjamin L; Shi, Ling Fang; Kao, Peter et al. (2016) Calcium activated K⁺ channels in the electroreceptor of the skate confirmed by cloning. Details of subunits and splicing. Gene 578:63-73
Grondin, Cynthia J; Davis, Allan Peter; Wiegers, Thomas C et al. (2016) Advancing Exposure Science through Chemical Data Curation and Integration in the Comparative Toxicogenomics Database. Environ Health Perspect 124:1592-1599
Yamada, Toshiki; Krzeminski, Mickael; Bozoky, Zoltan et al. (2016) Role of CBS and Bateman Domains in Phosphorylation-Dependent Regulation of a CLC Anion Channel. Biophys J 111:1876-1886
Hartig, Ellen I; Zhu, Shusen; King, Benjamin L et al. (2016) Cortisol-treated zebrafish embryos develop into pro-inflammatory adults with aberrant immune gene regulation. Biol Open 5:1134-41

Showing the most recent 10 out of 36 publications