Supplementary Figure 5: BRD9 and SS18-SSX regulate distinct gene sets in synovial sarcoma.

(a). Enriched gene sets for gene groups 1, 2, and 3 from Fig. 5b. (b). Schematic depicting experimental conditions in CRL7250 fibroblast cells used in RNA-seq experiments. (c). GSEA performed on RNA-seq experiments from conditions outlined in Supplementary Figure 5b. (d). Example tracks at an SS18-SSX fusion-dependent site (left) and bar graph of gene expression by RNA-seq (right) in SYO-1 at the FLRT2 locus. n = 2 independent samples for each ChIP-seq experiment. Bar represents mean RPKM of n = 2 RNA replicates for each condition with RPKM for each sample plotted as a dot. (e). Example tracks at SS18-SSX fusion-independent sites (left) and bar graphs of gene expression by RNA-seq (right) in SYO-1 at the SLC7A5 and SRM loci. n = 2 independent samples for each ChIP-seq experiment. Bar represents mean RPKM of n = 2 RNA replicates for each condition with RPKM for each sample plotted as a dot. (f). Violin plot of CERES scores for genes that changed with a significance of p-adjusted<1e-3 after 6 days of dBRD9 treatment in MOLM-13 cells. p-adjusted values are Benjamini-Hochberg adjusted Wald p-values, p-value between sets of genes was calculated by two-sided t-test. Violin plot shows kernel density estimation with data quartiles represented as lines, the data median is shown as a dot.