DOI: 10.5061/dryad.2v6wwpznv
title: Supplementary data for: Transposon mutagenesis identifies cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression

description: 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 P&lt;0.0001 and
 q&lt;0.05. 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.