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CANTATAdb 2.0: Expanding the Collection of Plant Long Noncoding RNAs

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Plant Long Non-Coding RNAs

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1933))

Abstract

Long non-coding RNAs (lncRNAs) are a class of potent regulators of gene expression that are found in a wide array of eukaryotes; however, our knowledge about these molecules in plants is very limited. In particular, a number of plant species with important roles in biotechnology, agriculture and basic research still lack comprehensively identified and annotated sets of lncRNAs. To address these shortcomings, we previously created a database of lncRNAs in 10 model species, called CANTATAdb, and now we are expanding this online resource to encompass 39 species, including three algae. The lncRNAs were identified computationally using publicly available RNA sequencing (RNA-Seq) data. Expression values, coding potential calculations and other types of information were used to provide annotations for the identified lncRNAs. The data are freely available for searching, browsing and downloading from an online database called CANTATAdb 2.0 (http://cantata.amu.edu.pl, http://yeti.amu.edu.pl/CANTATA/).

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Acknowledgments

This work was supported by the National Science Centre (grant No. 2014/15/D/NZ2/00525 to M.W.S); the KNOW Poznan RNA Centre (grant No. 01/KNOW2/2014); the Polish Ministry of Science and Higher Education (decision No. 1268/MOB/IV/2015/0 to M.W.S - Mobility Plus project).

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Authors and Affiliations

  1. Laboratory of Integrative Genomics, Institute of Anthropology, Adam Mickiewicz University, Poznan, Poland

    Michał Wojciech Szcześniak, Oleksii Bryzghalov, Joanna Ciomborowska-Basheer & Izabela Makałowska

Authors
  1. Michał Wojciech Szcześniak
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  2. Oleksii Bryzghalov
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  3. Joanna Ciomborowska-Basheer
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  4. Izabela Makałowska
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Corresponding author

Correspondence to Michał Wojciech Szcześniak .

Editor information

Editors and Affiliations

  1. Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, Guangxi, China

    Julia A. Chekanova  & Hsiao-Lin V. Wang  & 

  2. Department of Biology, Emory University, Atlanta, Georgia, USA

    Hsiao-Lin V. Wang

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Szcześniak, M.W., Bryzghalov, O., Ciomborowska-Basheer, J., Makałowska, I. (2019). CANTATAdb 2.0: Expanding the Collection of Plant Long Noncoding RNAs. In: Chekanova, J.A., Wang, HL.V. (eds) Plant Long Non-Coding RNAs. Methods in Molecular Biology, vol 1933. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9045-0_26

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  • DOI: https://doi.org/10.1007/978-1-4939-9045-0_26

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9044-3

  • Online ISBN: 978-1-4939-9045-0

  • eBook Packages: Springer Protocols

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