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Single-cell whole transcriptome sequencing denotes a new technique to amplify and sequence the whole transcriptome from the perspective of a single cell. It can be used to study the gene expression in individual cells, especially applicable in the highly heterogeneous stem cells, tumor cells and a small number of cell colonies of early embryo development. The single-cell transcriptome analysis is conducive to further study the processes of cell differentiation, cell reprogramming and transdifferentiation, as well as related gene regulatory network.