Supplementary Figure 2: Core regulatory TFs in RH4 cells with shRNA dissection of transcriptional networks.

a, Core regulatory (CR) SEs and TFs in RH4 cells. Data is from ChIP-seq of H3K27ac, and is representative of more than 10 replicate independent experiments in RH4 cell across different cell passage numbers that all gave very similar results. b, Portion of TFs with SEs are ranked by network connectivity (below); TFs with greater than 50% of max connectivity are classified as CR TFs in RH4 cells. c, Scatter plot of CRISPR dependency score and total connectivity; Top CR TFs are those with ≤-1 dependency. d, Rank order of gene expression plot for RH4 CR TFs, with top CR TFs (essential in RH4) highlighted. e, RNA-seq after depletion of CR TFs P3F, MYOD1, MYOG, SOX8 and MYCN with shRNA for 48 hours in RH4 cells. Each of these RNA-seq experiments was performed once, and similar results were obtained from orthogonal RNA-seq experiments after CRISPR disruption of these factors at multiple time points (see Fig. 2). f, Bubble plot summarizing the RNA-seq results for gene set enrichment with normalized enrichment score (NES, normalized for gene set size) and P-value calculated in GSEA which uses a Kolmogorov-Smirnov test comparing the enrichment score to the null distribution estimated from 1,000 random permutations. g, Example GSEA plots from (f).