Clonally selected SB insertions affect trunk driver proto-oncogene expression in SB-cuSCC genomes.

(A) Summary of Zmiz1 and Zmiz2 transcripts identified from bulk analysis of cuSCC cells by wtRNA-seq are represented as the log₁₀ ratio of fragments per kilobase of transcript per million (FPKM) from the average of 6 genomes with SB insertions into Zmiz1 compared to the transcripts from the single genome with Zmiz2 SB insertion, defined by FPKM mapped reads from ribo-depleted RNA. (B) Transcripts identified from bulk analysis of cuSCC cells by wtRNA-seq are represented as the log₁₀ ratio of SB insertion containing compared to wild-type transcripts, defined by fragments per kilobase of transcript per million mapped reads from ribo-depleted. (C-F) Individual panels from Fig 5E: multifold induction of gene expression in cuSCC masses with (+) high read depth activating SB insertion events among 4 candidate oncogenic drivers compared with normal gene expression levels in cuSCC tumors without (–) SB insertions.

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