Supplementary Figure 3: Replicative analysis of the SHEP-21N system and the dynamics of the tet-on MYCN SHEP system. | Nature Genetics

Supplementary Figure 3: Replicative analysis of the SHEP-21N system and the dynamics of the tet-on MYCN SHEP system.

From: Enhancer invasion shapes MYCN-dependent transcriptional amplification in neuroblastoma

Supplementary Figure 3

a, Left, differential analysis volcano plot of two ChIP–seq replicates comparing the log2 fold change at 2 h versus log10 P value. Blue and red circles denote distal and TSS MYCN sites, respectively. Right, box plot representation of differential regions (P < 0.1, fold change > log2 0.5) showing the log2 fold change at MYCN TSSs and distal sites. b, Left, differential analysis volcano plot of two ChIP–seq replicates comparing the log2 fold change at 24 h versus log10 P value. Blue and red circles denote distal and TSS MYCN sites, respectively. Right, box plot representation of differential regions (P < 0.1, fold change > log2 0.5) showing the log2 fold change at MYCN TSSs and distal sites. c, Scatter of MYCN peak AUC between MYCN ChIP–seq replicates at 0, 2, and 24 h after MYCN shutdown. Pearson correlation is noted. d, Box plots of the log2 fold change of MYCN load at the TSSs and distal enhancers of the top 5,000 genes ranked by proximal MYCN signal. Left, ChIP-Rx before scaling. Right, ChIP-Rx after scaling. e, Heatmap and meta plot of MYCN signal at promoters (left) and enhancers (right) upon MYCN induction in the tet-on MYCN SHEP cell line. Each row shows the ±5-kb region centered on the TSS or enhancer ranked by average H3K27ac signal. Color scaled intensities are in units of RPM/bp. f, Heatmap and meta plot of H3K27ac signal at promoters (left) and enhancers (right) upon MYCN induction in the tet-on MYCN SHEP cell line. Each row shows the ±5-kb region centered on the TSS or enhancer ranked by average H3K27ac signal. Color scaled intensities are in units of RPM/bp. g, Box plots of MYCN (red) and H3K27ac (blue) ChIP–seq signal (RPM/bp) at active promoters and enhancers at 0, 2, and 6 h after MYNC induction. Significant differences are denoted (Welch’s two-tailed t test): ***P < 1 × 10–9.

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