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. 2020 Dec 23;4(2):e202000808. doi: 10.26508/lsa.202000808

Figure 1. BAF complex is organized in unusually broad domains in primary synovial sarcoma organoids.

Figure 1.

(A) Micrographs show the four patient-derived synovial sarcoma 3D organoid cultures. Scale bar: 200 μm. (B) Schematic representation of the SS18-SSX fusion gene (left) and RT-PCR products showing the detection of SS18-SSX in patient-derived synovial sarcoma organoids. Water is used as a negative control and HSSYII cell line as a positive control. (C) H3K36me3 ChIP-seq signals at the SSX1 locus show active transcription of the 3′ terminal region that becomes fused to SS18 to form the fusion gene SS18-SSX in patient-derived synovial sarcoma organoids. (D) Violin plots show the overall distribution of peak widths for SMARCA2/4–binding sites in four synovial sarcoma patient-derived tumor organoids, two Ewing sarcoma patient-derived tumor organoids (EwS1 and 2) and four control cell types. (E, F) Boxplots show the distribution of peak widths of the (E) broadest BAF complex domains (Q4) and the (F) narrowest BAF complex domains (Q1) identified in each cell type separately. (G) Pie charts show the genomic locations of SMARCA2/4–binding sites in four synovial sarcoma patient-derived tumor organoids. (H) Examples of broad BAF complex domains identified in synovial sarcoma at loci associated with BMP4 and SOX2. See also Fig S1.