Sci-fate characterizes the dynamics of gene expression in single cells

Gene expression programs change over time, differentiation and development and in response to stimuli. However, nearly all techniques for profiling gene expression in single cells do not directly capture transcriptional dynamics. Here, we present a method for combined single-cell combinatorial indexing and mRNA labelling (sci-fate), which uses combinatorial cell indexing and 4sU labeling of newly synthesized mRNA to concurrently profile the whole and newly synthesized transcriptome in each of many single cells. We used sci-fate to study the cortisol response in >6,000 single cultured cells. From these data, we quantified the dynamics of the cell cycle and of glucocorticoid receptor activation, and explored their intersection. Finally, we developed software to infer and analyze cell state transitions. We anticipate that sci-fate will be broadly applicable to quantitatively characterize transcriptional dynamics in diverse systems.