Fig. 2

SLAM-seq shows that most genes expressed during zebrafish MZT are both maternally and zygotically expressed. A Representation of experimental setup and SLAM-seq time course covering 8 h of early zebrafish development, embryo developmental stages represented in the x-axis. B, C Sinaplots showing mean zygotic component score (labeled reads/total reads) for pure maternal, pure zygotic, and maternal-zygotic genes in all SLAM-seq time points. Number of expressed genes in each category (>5 mean CPMs, counts per million, nd = non-detected) is shown below each time point. Bonferroni corrected p-values from one-sided Wilcoxon tests were as follows: *** < 0.0001, ** < 0.001, * < 0.05, ns ≥ 0.05. D Stacked bar plots showing the percentage of expressed genes (>5 mean counts per million, CPMs) without labeled mRNAs (pure maternal) and with some level of labeling in each timepoint. Number of genes in each category colored accordingly. * False positives, as explored in Additional file 3: Fig. S2C. E Venn diagrams showing all protein coding genes from the nuclear genome or only non-coding transcripts, number of genes, and their percent total are shown within each diagram, p-values from chi-square tests are shown