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RNA Sequencing Data Analysis on the Maser Platform and the Tag-Count Comparison Graphical User Interface

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Cancer Drug Resistance

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2535))

Abstract

The RNA sequencing (RNA-seq) process that allows for comprehensive transcriptome analysis has become increasingly simple. Analysis and interpretation of RNA-seq output data are indispensable for research, but bioinformatics experts are not always available to assist. Currently, however, even a wet-lab specialist can perform the pipeline analysis of RNA-seq described in this chapter using the Maser platform and the Tag-Count Comparison Graphical User Interface (TCC-GUI). These are free of charge for scientific use.

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Acknowledgments

The authors declare no conflict of interest and financial disclosure. We would like to pay tribute and thanks to the developers of all the tools introduced in this chapter.

Maser. Copyright (C) 2009-2020 National Institute of Genetics. All right reserved. https://cell-innovation.nig.ac.jp

R. The R logo is (C) 2016 The R Foundation. Released under the terms of the Creative Commons Attribution-ShareAlike 4.0 International License (CC-BY-SA 4.0). https://www.r-project.org

RStudio™. RStudio™ and Shiny™ are trademarks of RStudio, PBC. Released under the provisions of the CNU Affero General Public License version 3 (AGPL v.3). https://rstudio.com

TCC-GUI. Copyright (C) 2020 Bioinformation Engineering Lab, Graduate School of Agricultural and Life Sciences/Faculty of Agriculture, The University of Tokyo. Released under the MIT license. https://infinityloop.shinyapps.io/TCC-GUI/.

Computations were partially performed on the NIG supercomputer at ROIS National Institute of Genetics.

Portions of this work were presented at the second annual meeting of Kyushu Neuro-Oncology Study Group, Saga-City, Saga, Japan, on October 6, 2019.

This work was supported by JSPS and the Hungarian Academy of Sciences under the Japan-Hungary Research Cooperative Program (to Y.M.) and, in part, by Grants-in-Aid for Scientific Research (Fostering Joint International Research) 20KK0254 (to Y.M.), and by Grants-in-Aid for Scientific Research from JSPS KAKENHI (C)17K10839 (to K.U.), (C) 20K09351(to Y.M.), and (C)21K09154 (to K.U.), and by Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research; BINDS) from AMED under Grant Number JP17am0101001.

The authors would like to thank Enago (www.enago.jp) for the English language review.

Author information

Authors and Affiliations

  1. Department of Neurosurgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan

    Kenta Ujifuku

  2. Department of Neurosurgery, Nagasaki University Hospital, Nagasaki, Japan

    Yoichi Morofuji

  3. Biomedical research support center, Nagasaki University School of Medicine, Nagasaki, Japan

    Hiroshi Masumoto

Authors
  1. Kenta Ujifuku
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  2. Yoichi Morofuji
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  3. Hiroshi Masumoto
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Corresponding author

Correspondence to Kenta Ujifuku .

Editor information

Editors and Affiliations

  1. Department of Oncology and Molecolar Medicine, Istituto Superiore di Sanità, Rome, Italy

    Marta Baiocchi

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© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Ujifuku, K., Morofuji, Y., Masumoto, H. (2022). RNA Sequencing Data Analysis on the Maser Platform and the Tag-Count Comparison Graphical User Interface. In: Baiocchi, M. (eds) Cancer Drug Resistance. Methods in Molecular Biology, vol 2535. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2513-2_13

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  • DOI: https://doi.org/10.1007/978-1-0716-2513-2_13

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2512-5

  • Online ISBN: 978-1-0716-2513-2

  • eBook Packages: Springer Protocols

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