Live organism transcriptomics

Recent research employing live-cell transcriptomics has demonstrated measurement of the temporal changes of gene expression from single cells cultured in vitro. However, the time-series analyses and demonstration of the in vivo applicability remain unexplored. Here, we show that our nanoelectrokinetic sampling uniquely enables live-cell and live-organism transcriptomics at multiple time points to uncover the individuality of dynamic gene expression in single cells and organisms. The autoregression with the live-cell transcriptome offers inference of single-cell gene regulation networks, which provide solid mechanisms for stochastic behaviors of individual cells. Live-organism transcriptome captured fate-specific mRNA kinetics in the embryonic development of nematode Caenorhabditis elegans, identifying the core determinant of stochastic fate bifurcation. These results highlight the power of real-time-series transcriptomics to comprehend the dynamical individuality and the stochastic process of fate determination. We anticipate our study will be a starting point for understanding the spontaneous individualization of living matters from single cells to organisms, contributing to the elucidation of fundamental laws in the diversification of life.