REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Human mucosal samples taken from the whole bladder of two individuals and representative mucosal samples taken from seven individuals	UT MD Anderson Cancer Center	Nine human bladder maps. See Table S1
Critical commercial assays
Whole Exome Sequencing on Illumina NovaSeq 6000 Platform	Illumina	N/A
Illumina Infinium Omni2.5-8 BeadChips for CNV	Illumina	GPL16104
Infinium MethylationEPIC BeadChip Kit	Illumina	GPL21145
Deposited data
RNAseq raw and analyzed data	This paper	SRA: PRJNA736323
Exom Sequencing raw and analyzed data	This paper	SRA: PRJNA736323
CNV raw and analyzed data	This paper	GEO: GSE171363
Methylation raw and analyzed data	This paper	GEO: GSE171363
Human reference NCBI build 38, GRCh38	Genome Reference Consortium	https://www.ncbi.nlm.nih.gov/assembly/grc/human
Human Genome Browser, GRCh38	University of California Santa Cruz Genomic Institute	https://genome.ucsc.edu/cgi-bin/hgGateway
TCGA mutational data	Broad Institute Genome Data Analysis Centers TCGA	http://gdac.broadinstitute.org/
RNASeq level 3 data, Illumina methylation array 450 and SNP6 CNV	R package TCGAGeneReport (version 2.3)	http://gdac.broadinstitute.org/
Mutational signatures	Alexandrov et al., 2013	http://cancer.sanger.ac.uk/cosmic/signatures
Oligonucleotides	This paper	See Table S8
Software and algorithms
RSeQC software	Wang et al., 2012	http://rseqc.sourceforge.net/
FastQC software	N/A	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
FeatureCounts software in the Subread package	Liao et al., 2014	http://subread.sourceforge.net/
DESeq2 software (version 1.26.0)	Love et al., 2014	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Illumina GenomeStudio software (version 2.0)	N/A	https://support.illumina.com/downloads/genomestudio-2-0.html
OncoSNP software	Yau et al., 2010	https://sourceforge.net/projects/oncosnp/
minfi R package (version 1.30.0)	Aryee et al., 2014; Fortin et al., 2014	https://bioconductor.org/packages/release/bioc/html/minfi
Significance analysis of microarray (SAM)	Tusher et al., 2001	https://tibshirani.su.domains/SAM/
BWA-MEM (version 0.7.12)	Li and Durbin, (2010).	http://bio-bwa.sourceforge.net/
Samtools (version 1.4)	Etherington et al., 2015	http://samtools.sourceforge.net
Picard (version 2.5.0)	N/A	https://broadinstitute.github.io/picard
GATK (version 4.1.3.0)	McKenna et al., 2010	https://software.broadinstitute.org/gatk/download
MuTect2	DePristo et al., 2011; Cai et al., 2016	https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php
Oncotator (version 0.8.0)	Ramos et al., 2015	http://portals.broadinstitute.org/oncotator
Parsimony method	Nixon, 1999; Paradis, 2011)	https://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/Phylogenetics/phylo14.html
Ingenuity Pathway Analysis (IPA)	Jiménez-Marin et al., 2009; Krämer et al., 2014	https://www.qiagen.com/us/products/life-science-research/research-applications/gene-expression-analysis/analysis/ingenuity-pathway-analysis/
Gene set enrichment analysis (GSEA)	Subramanian et al., 2005	https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page