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.

Original languageEnglish
Title of host publicationInnovations in Nephrology
Subtitle of host publicationBreakthrough Technologies in Kidney Disease Care
PublisherSpringer International Publishing
Number of pages16
ISBN (Electronic)9783031115707
ISBN (Print)9783031115691
StatePublished - Jan 1 2022


  • High-throughput nucleotide sequencing
  • Kidney diseases
  • Organoids
  • RNA sequence analysis
  • Single-cell analysis


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