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Transcriptomic Analysis of Human Naïve and Primed Pluripotent Stem Cells

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Human Naïve Pluripotent Stem Cells

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2416))

Abstract

Over the last decade, RNA-Sequencing (RNA-Seq) has revolutionized the field of transcriptomics due to its sheer advantage over previous technologies for studying gene expression. Even the domain of stem cell bioinformatics has benefited from these advancements. It has helped look deeper into how the process of pluripotency is maintained by stem cells and how it may be exploited for application in regenerative medicine. However, as it is still an evolving technology, there is no single accepted protocol for RNA-Seq data analysis. From a wide array of tools and/or algorithms available for the purpose, researchers tend to develop a pipeline that is best suited for their sample, experimental design, and computational power. In this tutorial, we describe a pipeline based on open-source tools to analyze RNA-Seq data from naïve and primed state human pluripotent stem cell samples. Precisely, we show how RNA-Seq data can be downloaded from databases, processed, and used to identify differentially expressed genes and construct a co-expression network. Further, we also show how the list of interesting genes obtained from differential expression testing or co-expression network be analyzed to gain biological insights.

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Acknowledgments

This work was supported by the Department of Biotechnology (DBT), Government of India (Grant No. BT/PR12842/BID/7/521/2015).

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Authors and Affiliations

  1. Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj, India

    Arindam Ghosh & Anup Som

Authors
  1. Arindam Ghosh
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  2. Anup Som
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Editors and Affiliations

  1. Babraham Institute, Cambridge, UK

    Peter Rugg-Gunn

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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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Ghosh, A., Som, A. (2022). Transcriptomic Analysis of Human Naïve and Primed Pluripotent Stem Cells. In: Rugg-Gunn, P. (eds) Human Naïve Pluripotent Stem Cells. Methods in Molecular Biology, vol 2416. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1908-7_14

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  • DOI: https://doi.org/10.1007/978-1-0716-1908-7_14

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1907-0

  • Online ISBN: 978-1-0716-1908-7

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