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tRex: A Web Portal for Exploration of tRNA-Derived Fragments in Arabidopsis thaliana.
Plant Cell Physiol. 2018 Jan 01; 59(1):e1.PC

Abstract

tRNA-derived fragments (tRFs) constitute a new class of short regulatory RNAs that are a product of nascent or mature tRNA processing. tRF sequences have been identified in all domains of life; however, most published research pertains to human, yeast and some bacterial organisms. Despite growing interest in plant tRFs and accumulating evidence of their function in plant development and stress responses, no public, web-based repository dedicated to these molecules is currently available. Here, we introduce tRex (http://combio.pl/trex)-the first comprehensive data-driven online resource specifically dedicated to tRFs in the model plant Arabidopsis thaliana. The portal is based on verified Arabidopsis tRNA annotation and includes in-house-generated and publicly available small RNA sequencing experiments from various tissues, ecotypes, genotypes and stress conditions. The provided web-based tools are designed in a user-friendly manner and allow for seamless exploration of the data that are presented in the form of dynamic tables and cumulative coverage profiles. The tRex database is connected to external genomic and citation resources, which makes it a one-stop solution for Arabidopsis tRF-related research.

Authors+Show Affiliations

Department of Computational Biology, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan, 61-614 Poznan, Poland.Department of Computational Biology, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan, 61-614 Poznan, Poland.Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan, 61-614 Poznan, Poland.Department of Computational Biology, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan, 61-614 Poznan, Poland.Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan, 61-614 Poznan, Poland.Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan, 61-614 Poznan, Poland.Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan, 61-614 Poznan, Poland.Department of Computational Biology, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan, 61-614 Poznan, Poland.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

29145635

Citation

Thompson, Agnieszka, et al. "TRex: a Web Portal for Exploration of tRNA-Derived Fragments in Arabidopsis Thaliana." Plant & Cell Physiology, vol. 59, no. 1, 2018, pp. e1.
Thompson A, Zielezinski A, Plewka P, et al. TRex: A Web Portal for Exploration of tRNA-Derived Fragments in Arabidopsis thaliana. Plant Cell Physiol. 2018;59(1):e1.
Thompson, A., Zielezinski, A., Plewka, P., Szymanski, M., Nuc, P., Szweykowska-Kulinska, Z., Jarmolowski, A., & Karlowski, W. M. (2018). TRex: A Web Portal for Exploration of tRNA-Derived Fragments in Arabidopsis thaliana. Plant & Cell Physiology, 59(1), e1. https://doi.org/10.1093/pcp/pcx173
Thompson A, et al. TRex: a Web Portal for Exploration of tRNA-Derived Fragments in Arabidopsis Thaliana. Plant Cell Physiol. 2018 Jan 1;59(1):e1. PubMed PMID: 29145635.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - tRex: A Web Portal for Exploration of tRNA-Derived Fragments in Arabidopsis thaliana. AU - Thompson,Agnieszka, AU - Zielezinski,Andrzej, AU - Plewka,Patrycja, AU - Szymanski,Maciej, AU - Nuc,Przemyslaw, AU - Szweykowska-Kulinska,Zofia, AU - Jarmolowski,Artur, AU - Karlowski,Wojciech M, PY - 2017/08/23/received PY - 2017/11/13/accepted PY - 2017/11/18/pubmed PY - 2018/8/14/medline PY - 2017/11/18/entrez KW - Arabidopsis thaliana KW - Database KW - Web portal KW - sRNA-seq KW - tRF KW - tRNA-derived fragments SP - e1 EP - e1 JF - Plant & cell physiology JO - Plant Cell Physiol VL - 59 IS - 1 N2 - tRNA-derived fragments (tRFs) constitute a new class of short regulatory RNAs that are a product of nascent or mature tRNA processing. tRF sequences have been identified in all domains of life; however, most published research pertains to human, yeast and some bacterial organisms. Despite growing interest in plant tRFs and accumulating evidence of their function in plant development and stress responses, no public, web-based repository dedicated to these molecules is currently available. Here, we introduce tRex (http://combio.pl/trex)-the first comprehensive data-driven online resource specifically dedicated to tRFs in the model plant Arabidopsis thaliana. The portal is based on verified Arabidopsis tRNA annotation and includes in-house-generated and publicly available small RNA sequencing experiments from various tissues, ecotypes, genotypes and stress conditions. The provided web-based tools are designed in a user-friendly manner and allow for seamless exploration of the data that are presented in the form of dynamic tables and cumulative coverage profiles. The tRex database is connected to external genomic and citation resources, which makes it a one-stop solution for Arabidopsis tRF-related research. SN - 1471-9053 UR - https://www.unboundmedicine.com/medline/citation/29145635/tRex:_A_Web_Portal_for_Exploration_of_tRNA_Derived_Fragments_in_Arabidopsis_thaliana_ L2 - https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/pcx173 DB - PRIME DP - Unbound Medicine ER -