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Single Cell Transcriptomics

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Innovations in Nephrology

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Abstract

Kidney is a highly complex organ comprised of diverse cell types and subpopulations. This cellular complexity complicates efforts to understand both physiology and disease mechanisms. The recent advent of single-cell RNA sequencing (scRNA-seq) technologies has enabled us to dissect the cellular heterogeneity of kidney in unprecedented detail by profiling transcriptomic signatures at single-cell resolution. In addition to the widely used droplet microfluidics-based approaches, other alternative methods such as split-pool barcoding are emerging with substantially enhanced throughput and cost efficiency. Furthermore, evolving complementary technologies such as single-cell epigenetic profiling are now being leveraged together with scRNA-seq to describe comprehensive gene regulatory networks. Cell-specific transcriptomic characterizations of both mouse and human kidneys allow us to gain a comprehensive picture of biological processes in healthy and diseased kidneys. Successful application of scRNA-seq to biosamples including urine cells suggests possible future applications in diagnostics and precision medicine. The maturation of widely available bioinformatic tools now enables any researcher to utilize scRNA-seq without a deep background in informatics or computer science. Indeed, a basic understanding of single-cell omics and computational methods is increasingly becoming essential for investigators. In this chapter, we review the fundamentals of scRNA-seq methods, data analysis and future opportunities for scRNA-seq in nephrology.

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Author notes

  1. Yoshiharu Muto and Haikuo Li contributed equally with all other contributors.

Authors and Affiliations

  1. Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St Louis, MO, USA

    Yoshiharu Muto, Haikuo Li & Benjamin D. Humphreys

  2. Department of Developmental Biology, Washington University in St. Louis School of Medicine, St Louis, MO, USA

    Benjamin D. Humphreys

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  1. Yoshiharu Muto
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  2. Haikuo Li
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Correspondence to Benjamin D. Humphreys .

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  1. School of Medicine, University of Fortaleza, Fortaleza, Ceará, Brazil

    Geraldo Bezerra da Silva Junior

  2. Division of Nephrology and Endocrinology, University of Tokyo School of Medicine, Tokyo, Japan

    Masaomi Nangaku

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Muto, Y., Li, H., Humphreys, B.D. (2022). Single Cell Transcriptomics. In: Bezerra da Silva Junior, G., Nangaku, M. (eds) Innovations in Nephrology. Springer, Cham. https://doi.org/10.1007/978-3-031-11570-7_5

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