Extended Data Figure 4

a,b. For genes that are observed only outside of the steady state, such as genes upregulated late in the chromaffin differentiation (a) or down-regulated early in the Schwann cell precursors (b), gene-relative γ fit will likely deviate from its steady-state value. c,d. To correct for such effects, a structure-based γ fit will first predict γ for every gene based on its structural parameters, and then use k most correlated genes in the dataset to adjust M-value (M = log₂[u_o/u_ss], where u_ss is the unspliced counts predicted from spliced counts under steady-state, and u_o is the observed unspliced count) using robust mean, and re-estimate γ. e. Scatter-plot comparing gene-relative and structure-based γ estimates, with colored circles highlighting γ adjustments for genes down-regulated early in SCPs (blue) and up-regulated late in chromaffin cells (green). The values are shown on a natural log scale. f-i. Cell expression velocity in the chromaffin E12.5 dataset, based on the structure-based γ estimates, shown on the first five PCs.