Fig. 5

Computational analysis of high-confidence PMC CRMs. a ATAC-seq differential peaks (green rectangles) and DNase-seq differential peaks (violet rectangles) near Sp-p16 and Sp-mitf, both PMC DE genes. Aligned reads averaged across replicates, from isolated PMCs (light green trace) and non-PMC cells (dark green trace) using ATAC-seq, and control 28 hpf embryos (violet trace) and PMC (−) embryos (dark purple trace) using DNase-seq, are shown. b Temporal expression profiles (Tu et al., 2012) of 420 PMC DE genes identified previously (Rafiq et al., 2014). Each gene is represented by a single row. The color scale ranges from deep red (2.5-fold higher than mean expression) to deep blue (2.5-fold lower than mean expression). White indicates mean expression. Four clusters are delineated, corresponding to maximal gene expression at 0–10, 40–72, 24–40 and 18–24 hpf, respectively. c Temporal expression of the 62 PMC DE genes within 10 kb of overlapping differential peaks: these PMC DE genes were classified into four clusters, delineated in Fig. 3b. d PMC DE genes were classified into categories based on levels of gene expression in isolated PMCs (data obtained from (Rafiq et al., 2014). “High” expression genes: FPKM between 2512 and 100 (top 17% of all 420 DE genes); “very low” expression genes: FPKM between 14 and 0 (bottom 25% of all 420 DE genes)