Abstract
Cell-to-cell variation and heterogeneity are fundamental and intrinsic characteristics of stem cell populations, but these differences are masked when bulk cells are used for omic analysis. Single-cell sequencing technologies serve as powerful tools to dissect cellular heterogeneity comprehensively and to identify distinct phenotypic cell types, even within a ‘homogeneous’ stem cell population. These technologies, including single-cell genome, epigenome, and transcriptome sequencing technologies, have been developing rapidly in recent years. The application of these methods to different types of stem cells, including pluripotent stem cells and tissue-specific stem cells, has led to exciting new findings in the stem cell field. In this review, we discuss the recent progress as well as future perspectives in the methodologies and applications of single-cell omic sequencing technologies.
Highlights
An individual cell is the smallest functional and universal unit of organisms
Single-cell RNA-seq analysis has revealed that many genes have variable expression among individual mouse embryonic stem cells [18, 19] and, importantly, has identified sub-populations that have distinct transcriptomes [23, 65, 66]
Like the work of Treutlein et al [49], these two studies again demonstrate that the single-cell RNA-seq approach can provide a snapshot of the transcriptome dynamics of a developmental process if reasonable numbers of individual cells of the population are sequenced at a given time point
Summary
An individual cell is the smallest functional and universal unit of organisms. Gene expression is regulated within or between individual cells, and so, ideally, analyses of gene expression would be performed using single cells; but owing to technical limitations, such as the tiny size of an individual cell, most of the gene-expression studies described in the literature (especially those at a wholegenome scale) have been performed using bulk samples of thousands or even millions of cells. FACS fluorescence-activated cell sorting, FISSEQ fluorescence in situ sequencing, FRISCR fixed and recovered intact single-cell RNA, MALBAC multiple annealing and looping-based amplification cycles, MARS massively parallel single-cell RNA-sequencing, PCR polymerase chain reaction, PMA Phi29-mRNA amplification, sc single-cell, seq sequence, SMA semirandom primed PCR-based mRNA transciptome amplification, STRT-seq single-cell tagged reverse transcription, TIVA transcriptome in vivo analysis, UMI unique molecular identifier early mammalian embryos [43,44,45,46,47,48], developing tissues [33, 49,50,51], adult tissues [22, 36, 37, 52, 53], immune cells [20, 21, 54,55,56], cancer cells [6, 57,58,59], and stem cells that are either isolated in vivo [39, 60,61,62,63] or cultured in vitro [23, 38, 64,65,66,67].
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