Fig. 3

SLAM-seq reveals timely coordination of transcriptional onset of genes during zebrafish maternal-to-zygotic transition. A Schematic representation of previously determined transcription waves depended and in-depended on zygotic products during zebrafish development (top, Lee et al., 2013). Sinaplots showing the mean zygotic counts per million (zCPMs) for each hour, only once per gene (at the time >1 zCPM is detected) for waves depended and in-depended on zygotic products, plus all other detected transcribed genes (gray). Black bars represent mean values for each group, and total number of genes in each timepoint is shown below each group. B Schematic representation of hourly grouped transcription output events during zebrafish development, regardless of when within each hour they were activated (top). Sinaplots showing the mean zygotic counts per million (zCPMs) for each hour, only once per gene (at the time >1 zCPM is detected) for maternal-zygotic and zygotic genes (Fig. 2D). Black bars represent mean values for each group, and total number of genes in each timepoint is shown below each group. C Dendrogram showing the expression dynamics of transcriptional output throughout zebrafish development. Positive line slope indicates positive fold changes (fold change ≥ log2(1.5), adjusted p-value ≤ 0.2), negative slope indicates negative fold changes (fold change ≤ -log2(1.5), adjusted p-value ≤ 0.2), flat lines (slope = 0) indicate all other genes (> −log2(1.5) and < log2(1.5) or adjusted p-value > 0.2)