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

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<0.0001 and
q<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.