Advertisement

Usage of Single-Cell RNA Sequencing to Unveil Immune Lymphoid Cell Precursors

  • Yong YuEmail author
  • Pengtao LiuEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1884)

Abstract

Single-cell RNA sequencing (scRNA-seq) is a powerful tool to study immune cells, which enables an unbiased way to discover novel cell populations, biological meaningful cellular heterogeneity, and cell lineage development trajectories. Advances in scRNA-seq technologies and computational data analysis have driven a revolution in our understanding of the immune system in health and disease. Technically, the key step for scRNA-seq analysis is making a high-quality cDNA library for sequencing. Here, we describe a plate-based protocol to prepare single-cell cDNA library of bone marrow innate lymphoid precursors for next generation sequencing-based transcriptome analysis.

Key words

scRNA-seq Innate lymphoid cells Cellular heterogeneity Immune cell development PD-1 

References

  1. 1.
    Eberl G, Colonna M, Di Santo JP, McKenzie ANJ (2015) Innate lymphoid cells: A new paradigm in immunology. Science 348(6237):aaa6566.  https://doi.org/10.1126/science.aaa6566CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Artis D, Spits H (2015) The biology of innate lymphoid cells. Nature 517(7534):293–301.  https://doi.org/10.1038/nature14189CrossRefPubMedGoogle Scholar
  3. 3.
    Spits H, Artis D, Colonna M, Diefenbach A, Di Santo JP, Eberl G, Koyasu S, Locksley RM, McKenzie ANJ, Mebius RE, Powrie F, Vivier E (2013) Innate lymphoid cells - a proposal for uniform nomenclature. Nat Rev Immunol 13(2):145–149.  https://doi.org/10.1038/nri3365CrossRefPubMedGoogle Scholar
  4. 4.
    Schroder K, Hertzog PJ, Ravasi T, Hume DA (2004) Interferon-gamma: an overview of signals, mechanisms and functions. J Leukoc Biol 75(2):163–189.  https://doi.org/10.1189/jlb.0603252CrossRefPubMedGoogle Scholar
  5. 5.
    Constantinides M, McDonald B, Verhoef P, Bendelac A (2014) A committed hemopoietic precursor to innate lymphoid cells. Nature 508 (7496), 397–401CrossRefGoogle Scholar
  6. 6.
    Yu Y, Tsang JC, Wang C, Clare S, Wang J, Chen X, Brandt C, Kane L, Campos LS, Lu L, Belz GT, McKenzie AN, Teichmann SA, Dougan G, Liu P (2016) Single-cell RNA-seq identifies a PD-1(hi) ILC progenitor and defines its development pathway. Nature 539(7627):102–106.  https://doi.org/10.1038/nature20105CrossRefPubMedGoogle Scholar
  7. 7.
    Neu KE, Tang Q, Wilson PC, Khan AA (2017) Single-cell genomics: approaches and utility in immunology. Trends Immunol 38(2):140–149.  https://doi.org/10.1016/j.it.2016.12.001CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Papalexi E, Satija R (2018) Single-cell RNA sequencing to explore immune cell heterogeneity. Nat Rev Immunol 18(1):35–45.  https://doi.org/10.1038/nri.2017.76CrossRefPubMedGoogle Scholar
  9. 9.
    Stubbington MJT, Rozenblatt-Rosen O, Regev A, Teichmann SA (2017) Single-cell transcriptomics to explore the immune system in health and disease. Science 358(6359):58–63.  https://doi.org/10.1126/science.aan6828CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Picelli S, Bjorklund AK, Faridani OR, Sagasser S, Winberg G, Sandberg R (2013) Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Methods 10(11):1096–1098.  https://doi.org/10.1038/nmeth.2639CrossRefPubMedGoogle Scholar
  11. 11.
    Picelli S, Faridani OR, Bjorklund AK, Winberg G, Sagasser S, Sandberg R (2014) Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 9(1):171–181.  https://doi.org/10.1038/nprot.2014.006CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji UniversityShanghaiChina
  2. 2.LKS Faculty of MedicineSchool of Biomedical Sciences, The University of Hong KongHong KongChina

Personalised recommendations