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Single-Cell Transcriptome Analysis of T Cells

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In Vitro Differentiation of T-Cells

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2048))

Abstract

Single-cell RNA-seq (scRNA-seq) has provided novel routes to investigate the heterogeneous populations of T cells and is rapidly becoming a common tool for molecular profiling and identification of novel subsets and functions. This chapter offers an experimental and computational workflow for scRNA-seq analysis of T cells. We focus on the analyses of scRNA-seq data derived from plate-based sorted T cells using flow cytometry and full-length transcriptome protocols such as Smart-Seq2. However, the proposed pipeline can be applied to other high-throughput approaches such as UMI-based methods. We describe a detailed bioinformatics pipeline that can be easily reproduced and discuss future directions and current limitations of these methods in the context of T cell biology.

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Authors and Affiliations

  1. Kirby Institute for Infection and Immunity, The University of New South Wales, Sydney, NSW, Australia

    Willem Van Der Byl, Simone Rizzetto, Jerome Samir, Curtis Cai, Auda A. Eltahla & Fabio Luciani

  2. School of Medical Sciences, The University of New South Wales, Sydney, NSW, Australia

    Willem Van Der Byl, Simone Rizzetto, Jerome Samir, Curtis Cai, Auda A. Eltahla & Fabio Luciani

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  1. Willem Van Der Byl
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  2. Simone Rizzetto
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  3. Jerome Samir
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  4. Curtis Cai
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  5. Auda A. Eltahla
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  6. Fabio Luciani
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Correspondence to Fabio Luciani .

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  1. Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan

    Shin Kaneko

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Van Der Byl, W., Rizzetto, S., Samir, J., Cai, C., Eltahla, A.A., Luciani, F. (2019). Single-Cell Transcriptome Analysis of T Cells. In: Kaneko, S. (eds) In Vitro Differentiation of T-Cells. Methods in Molecular Biology, vol 2048. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9728-2_16

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  • DOI: https://doi.org/10.1007/978-1-4939-9728-2_16

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