Abstract
Salamanders are an excellent model organism to study regenerative processes due to their unique ability to regenerate lost appendages or organs. Straightforward bioinformatics tools to analyze and take advantage of the growing number of “omics” studies performed in salamanders were lacking so far. To overcome this limitation, we have generated a comprehensive data repository for the red-spotted newt Notophthalmus viridescens, named newt-omics, merging omics style datasets on the transcriptome and proteome level including expression values and annotations. The resource is freely available via a user-friendly Web-based graphical user interface (http://newt-omics.mpi-bn.mpg.de) that allows access and queries to the database without prior bioinformatical expertise. The repository is updated regularly, incorporating new published datasets from omics technologies.
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Acknowledgment
This work was supported by the Max-Planck-Society, the Excellence Cluster Cardiopulmonary System (ECCPS), the University of Giessen-Marburg Lung Center (UGMLC), the Cell and Gene Therapy Center (CGT) of the University of Frankfurt, the DFG (SFB TRR81), and the German Center for Cardiovascular Research (DZHK). The authors would like to thank Marc Bruckskotten for his invaluable input for creating newt-omics and for preparation of the figures.
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Looso, M., Braun, T. (2015). Data Mining in Newt-Omics, the Repository for Omics Data from the Newt. In: Kumar, A., Simon, A. (eds) Salamanders in Regeneration Research. Methods in Molecular Biology, vol 1290. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2495-0_26
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DOI: https://doi.org/10.1007/978-1-4939-2495-0_26
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