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Figure 5 (A) Different transcription kinetics may lead to differences in apparent activation times (arrowheads) based on assay detection thresholds (gray line). Assuming similar degradation kinetics, transcripts with faster induction rates should accumulate to higher levels in response to BMP. (B-E) Uninjected and Opto-BMP-injected embryos were exposed to blue light for 30 min at high (~3.5 hpf, B,C) or shield stage (~6.75 hpf, D,E), and target gene expression in response to the resulting BMP signaling pulses (Figure 3C–E and Figure 3—figure supplement 1I,J) was quantified using NanoString technology (Figure 4). Maximum average transcript counts were determined, and are plotted against activation time (B,D) (Figure 2) or spatial range (C,E). Error bars represent standard error, gray lines represent linear fits, ρs = Spearman correlation coefficient, ρp = Pearson correlation coefficient. crabp2b is not included due to lack of significant induction. (F-L) All three target gene response repeats were fitted with a model of induction and decay (Materials and methods). The average induction constant (σ) is plotted against activation time (F), spatial range (G), or maximum transcript count (J). The average decay constant (λ) is plotted against activation time (H), range (I), or maximum transcript count (K). Error bars represent standard error, ρs = Spearman correlation coefficient, ρp = Pearson correlation coefficient. crabp2b is not included due to lack of significant induction. pSmad1/5/9 immunofluorescence (Figure 3) was fitted with a polynomial (gray line, L) and used as signaling input. (M-Z) Individual fits of transcriptional responses (Figure 4); closed circles represent averages of three data points, open circles represent individual data points, and gray lines represent individual fits of each repeat. See the Figure 5—source data 1 source data file for source data.