Fig. 2

DNase-seq sample preparation and sequence analysis. a S. purpuratus embryos were treated with U0126 at the 2-cell stage to obtain PMC (−) embryos. Control and U0126-treated embryos were cultured for 28 h at 15 °C in triplicate. Nuclei were isolated and DNase-seq was carried out. Sequence reads were analyzed by the bioinformatics pipeline shown in Additional file 1: Figure S1A. b An example of DNase-seq differential peaks. The differential peaks (yellow rectangles) are located near the WHL22.245306 transcript. The aligned reads for each replicate are visualized as traces, and the differences in peak magnitude are clear when comparing control whole embryos (violet peak trace) to PMC(−) embryos (dark purple trace). Nominal p-values for differential peaks are indicated. c Distribution of DNase-seq peaks in the RPS with respect to the closest gene. See Methods for definitions of peak locations. d Distribution of DNase-seq differential peaks with respect to the closest gene