Fig. 3

NMF decomposition of time-coursed iPS cell differentiation to neurons. (A) State × sample matrix of the decomposition from the super-enhancer RNA profiles. The x-axis and y-axis reflect the time points and corresponding cell states, respectively, while the darker band represents the greater preference of the cell state. (B) The time series plot was made by collapsing the biological replicates. Progressing patterns, which can be observed in both figures, are interpreted as the transition of cells from one state to another. State 0, 1, and 2 are named initial, secondary, and final state in the text, which correspond to iPS (day 0), neuroectodermal (day 6), and neuronal progenitor (day 18) cell types, respectively. Day 12 is neural stem cell, a mixed transition state composed mainly of the final state and partially of the secondary state