A b Supplemental Figure 1. (a) TERT mRNA quantification after siTERT knockdown compared to a non-targeting siRNA control (siNT) for the TCCSUP and UM-UC-3.

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a b Supplemental Figure 1. (a) TERT mRNA quantification after siTERT knockdown compared to a non-targeting siRNA control (siNT) for the TCCSUP and UM-UC-3 bladder cancer cell line. (b) Cell growth measured as the change in total cell number after 5 days of growth. Triplicates were run for each cell line and values are indicated as mean ± S.E.

Supplemental Figure 2. Comparison of the CCLE and Earl,et al Supplemental Figure 2. Comparison of the CCLE and Earl,et al. copy number data. CCLE data were generated using an Affymetrix SNP6.0 chip and Earl, et al. used Illumina BeadArrays. Pearson correlation was calculated for each of the 13 cell lines analyzed.

a b c MTAP deletion CDKN2A deletion CDKN2B deletion no yes no yes no Supplemental Figure 3. Analysis of chr 9p21 locus gene expression using data from the Cancer Cell Line Encyclopedia for (a) MTAP, (b) CDKN2A and (c) CDKN2B. Boxplots were generated using gene expression data extracted from CCLE_Expression_Entrez_2012-10-18.res downloaded from the CCLE website (http://www.broadinstitute.org/ccle/data). Samples included 15 cell lines: 253J, RT4, SW-780, UM-UC-1, UM-UC-3, 5637, HT-1197, HT-1376, J82, RT112, SCABER, SW-1710, T24, TCCSUP, VM-CUB-1. There is a trend towards reduced gene expression in lines with a homozygous deletion of the gene, however the small sample size prevents meaningful statistical testing.

Supplemental Figure 4. Bladder cancer genes (a) MTAP, (b) DMRTA1, (c) ELAVL2 and (d) IFNE deleted on chr 9p21 are altered in many cancers, including bladder, primarily by CNV loss. The results from the studies shown are taken from the cBioPortal for Cancer Genomics. The study with the highest frequency of alteration of each gene is indicated.