Cell lineXY11q WM WM793-P WM793-P Lu ABAB WM793:WM793-P2WM793:1205-Lu WM793 WM793:WM793-P1 Supplemental Figure S1. Ploidy of WM793 series. A, FISH analysis on the WM793 series using chromosome X (DXZ1), Y (DYZ1) and 11q probes. The number of copies of each probe (labelled with different flours) was counted in individual cells and averaged. B, flow cytometric analysis of the WM793 series. DNA content is reflected across the X-axis (propidium iodide staining). Cell counts are indicated on the Y-axis. To determine alteration in ploidy from the parental cells, the derivative cells were mixed at equal ratios with WM793 cells prior to flow sorting. Supplemental data S1. Gallagher et al.

Supplemental data S2. Gallagher et al. A B Supplemental Figure S2. A, Correlation curves for TaqMan LDAs for biological replicates of WM793, WM793-P1, WM793-P2 and 1205-Lu. Correlation coefficients range from 0.91 to B, Correlation between DNA microarrays and TaqMan LDAs. The Log 10 values of the fold difference for derivative cell lines compared to the parental WM793 cells are plotted. Data derived from DNA microarray experiments (Y axis) are plotted against TaqMan LDA experiments (X axis). The values in pink indicate genes that exhibit the same directionality in terms of altered gene expression, as compared to the parental cell lines, using both technologies. Blue indicates genes that exhibit different directionality between the two approaches. Spearman rho correlation coefficients range from 0.30 to 0.90 and all are significant Lu V WM793 Spearman’s rho correlation coefficient = 0.30, p=0.02 WM793-P1 V WM793 Spearman’s rho correlation coefficient = 0.90, p<0.001 WM793-P2 V WM793 Spearman’s rho correlation coefficient = 0.68, p<0.001

*** WM793 WM793 + DAC WM793-P1 WM793-P1 + DAC WM793-P2 WM793-P2 + DAC 1205-Lu 1205-Lu + DAC %5mC ABAB 1205-Lu 1205-Lu + DAC WM793-P2 WM793-P2 + DAC WM793-P1 WM793-P1 + DAC WM793 WM793 + DAC Supplemental Figure S3. Global DNA methylation status in the WM793 series. A, measurement of 5mC content by high performance capillary electrophoresis. B, 5mC content as a percentage of the total cytosine pool, mC peak area * 100/(mC peak area + C peak area). Results are expressed as mean values with standard errors of the mean represented by bars. A Student t test was performed for each comparison of untreated and DAC treated cells; *** indicates the difference is highly significant, as indicated by a P value < C C C C Supplemental data S3. Gallagher et al.

Biological Process GO slim categories in Genome transport metabolism biological process physiological process development cell communication cell cycle response to stress cell motility death Biological Process GO slim categories on Array transport metabolism biological process physiological process development cell communication cell cycle response to stress cell motility death motor activity transcription regulator activity nucleic acid binding molecular function unknown signal transducer activity binding catalytic activity transporter activity enzyme regulator activity structural molecule activity motor activity transcription regulator activity nucleic acid binding molecular function unknown signal transducer activity binding catalytic activity transporter activity structural molecule activity enzyme regulator activity Molecular Function GO slim categories in Genome Molecular Function GO slim categories in Array Cellular Component GO slim categories in GenomeCellular Component GO slim categories in Arrays cell extracellular region cellular component unknown external encapsulating structure unlocalised protein complex cell extracellular region cellular component unknown external encapsulating structure unlocalised protein complex Supplemental data S4. Gallagher et al. A B C D Supplemental Figure S4. Comparison of genes on the HuGeneFL array to the whole genome. Pie charts represent the (A) biological process, (B) molecular function, and (C) cellular component information, under Gene Onotology (GO) terminology, of cohort of genes in the whole genome and represented by the HuGeneFL array used in our studies. D, comparison of the number of genes per chromosome on the array compared to the number of genes per chromosome in the whole genome; and number of GO classes that the genes on each chromosome represent.