Supplementary data for: Transposon mutagenesis identifies cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression (Q6722734)

Supplementary Note 1: S1 Text: Oncogenomic comparisons between SB candidate Trunk driver genes and their direct orthologs in human Cancer Gene Census; Pyrosequencing analysis of SB-driven keratinocyte cancer models; References. Supplementary Figures 1-11: S1 Fig: Overview of genetic crosses to generate SB|Trp53|Onc3 mouse model. S2 Fig: SB insertion patterns in activated and inactivated drivers. S3 Fig: Evaluating the reproducibility of SBCapSeq results from bulk cuSCC and normal skin specimens. S4 Fig. Hierarchical two-dimensional clustering of recurrent events in cuKA and cuSCC. S5 Fig. Curated biological pathways and processes enriched within SB-induced cuSCC. S7 Fig: ZMIZ1 metagene within the TCGA Head Neck Squamous Cell Carcinoma (hnSCC) RNA-seq dataset. S8 Fig: Clonally selected SB insertions affect trunk driver proto-oncogene expression in SB-cuSCC genomes. S9 Fig: Clonally selected SB insertions affect trunk driver genes by inactivating expression in SB-cuSCC genomes. S10 Fig: CREBBP knockdown does not alter proliferation rate in cuSCC cell lines. S11 Fig: Gross photographs of cuSCC xenograft masses collected at necropsy showing robust TurboGFP expression. S12 Fig: SB T2/Onc3 TG.12740 allele donor position mapping and exclusion for SB Driver Analysis. Supplementary Tables 1-20: S1 Table: Tumor incidence and subgroup classifications by cohort. S2 Table: Specimen metafile data for projects sequenced using SBCapSeq protocol with Ion Torrent Proton sequencer. S3 Table: Discovery and progression SB Driver Analysis for cuSCC60_SBC. S4 Table: Trunk SB Driver Analysis for cuSCC60_SBC. S5 Table: Discovery and progression SB Driver Analysis for cuKA11_SBC. S6 Table: Trunk SB Driver Analysis for cuKA11_SBC. S7 Table: Discovery and progression SB Driver Analysis for cuSK32_SBC. S8 Table: SBCapSeq read depth and analysis for 4 cuSCC genomes selected for multi-region resequencing because they had intermixing of cuSCC and cuKA histologies. S9 Table: Enrichr gene set pathway enrichment analysis of cuSCC drivers. S10 Table: Summary of 7 cuSCC transcriptomes selected for whole transcriptome RNAseq analysis. S11 Table: BED file of SBfusion insertions in 7 cuSCC genomes by whole transcriptome RNAseq analysis. S12 Table: Venn diagram for overlap of genes with SBfusion reads detected by whole transcriptome RNAseq analysis and cuSCC60_SBC discovery driver. S13 Table: Venn diagram for overlap of genes with SBfusion reads detected by whole transcriptome RNAseq analysis and all cuSCC drivers. S14 Table: Transcripts per million (TPM) normalized whole transcriptome RNAseq values per gene from RNA isolated from cuSCC genomes with and without Zmiz1 insertions. S15 Table: Fragments Per Kilobase of Transcripts per Million (FPKM) normalized whole transcriptome RNAseq values per gene transcript from RNA isolated from cuSCC genomes with and without Zmiz1 insertions. S16 Table: Normalized microarray values per gene from RNA isolated from cuSCC genomes with and without Zmiz1 insertions. S17 Table: Normalized microarray values per probe from RNA isolated from cuSCC genomes with and without Zmiz1 insertions. S18 Table: All 289 genes with differential expression analysis from microarray data from RNA isolated from cuSCC genomes with and without Zmiz1 insertions with P0.0001 and q0.05. S19 Table: Lentiviral vectors containing shRNAs used in this study. S20 Table: TaqMan probes used in this study. Supplementary Datasets 1-5: S1 Data: BED file of SB insertions for cuSCC60_SBC. S2 Data: BED file of SB insertions for cuKA11_SBC. S3 Data: BED file of SB insertions for cuSK32_SBC S4 Data: BED file of SB insertions for 4 cuSCC genomes selected for multi-region resequencing because they had intermixing of cuSCC and cuKA histologies. S5 Data: Numerical data for graphs pertaining to Figure Panels Fig1A; Fig5A–E; Fig6A–B,D; Fig7C–G; Fig8A–B,D–F; Fig9A–I in the paper on the publicly availble PLOS Genetics Web site.