Additional file 6: of Systems analysis identifies miR-29b regulation of invasiveness in melanoma

Table (.csv) of Gene Ontology (GO) database terms used for the enrichment analysis of ‘epithelial-mesenchymal plasticity’ (EMP) and pigmentation processes in Fig. 3a, together with the number of genes within each category. As detailed in Methods/Databases, terms were identified by string matching and GO terms were excluded if they had less than five or more than 500 member genes. (CSV 5 kb

Additional file 5: of Systems analysis identifies miR-29b regulation of invasiveness in melanoma

Supporting Experimental Data (.pdf) – Contains: Table AF5.1, which lists the PCR primers used. Figure AF5.1 which displays baseline expression for genes of interest in a subset of LM-MEL melanoma cell lines using qPCR. Figure AF5.2, which displays siRNA transfection efficiency; Figure AF5.3, which displays additional qPCR results showing the effects of miR-29b mimic/inhibitor transfection. Figure AF5.4 & AF5.5, which display the effects of miR-29b mimic/inhibitor transfection on LM-MEL-77 cell proliferation and outgrowth. Figure AF5.6, which displays information to aid the reader’s interpretation of melanoma spheroid data. (PDF 3182 kb

Additional file 3: Figure S3. of Transketolase-like 1 ectopic expression is associated with DNA hypomethylation and induces the Warburg effect in melanoma cells

TKT and TKTL2 expression in melanoma cells. (A) TKT, (B) TKTL1 and (C) TKTL2 expression in LM-MEL-59 after treatment with two TKTL1 siRNAs or control siRNA for 72 h. Testis tissue was used as positive control for the expression of TKT, TKTL1 and TKTL2. (PPTX 69 kb

Additional file 2: Figure S1. of Iterative sorting reveals CD133+ and CD133- melanoma cells as phenotypically distinct populations

CD133+ and CD133- cells have similar frequency of tumour-initiating cells. Serial dilution of CD133+ and CD133- cell used in sub-cutaneous xenograft. Square, 105 cells; triangle, 104 cells; circle, 103 cells. Average (+/- SD) tumour volume measured over time, 3–5 mice/group. Data representative of 2 independent replicate experiments (PDF 203 kb

Additional file 5: Figure S5. of Transketolase-like 1 ectopic expression is associated with DNA hypomethylation and induces the Warburg effect in melanoma cells

TKTL1 expression in melanoma affects proliferation of cells. (A) Measurement of absorbance of LM-MEL-59 cells after TKTL1 siRNA or control siRNA treatment for 48 h by performing MTS assay. (B) Measurement of absorbance of LM-MEL-44 cells after overexpression of TKTL1 or empty vector for 48 h. (PPTX 57 kb

Additional file 1: Figure S1. of Transketolase-like 1 ectopic expression is associated with DNA hypomethylation and induces the Warburg effect in melanoma cells

TKTL1 is expressed in a subset of melanoma tumours and melanoma cell lines. (A) Representative staining patterns for TKTL1 in metastatic melanoma tumors are shown. Arrows indicate nuclear staining for Melanin. Original magnification, 200 Οm. (B) QRT-PCR for expression level of TKTL1 in a panel of 53 metastatic melanoma cell lines. (C) High magnification staining pattern of TKTL1 in melanoma cell line LM-MEL-59. Arrows indicate nuclear staining for Melanin. Original magnification, 200 Οm. (PPTX 1827 kb

Additional file 2: Figure S2. of Transketolase-like 1 ectopic expression is associated with DNA hypomethylation and induces the Warburg effect in melanoma cells

Correlation of TKTL1 gene expression with DNA methylation in melanoma patients. Exon expression data was compared to methylation patterns of TKTL1 and Spearman correlation coefficients were calculated. Methylation status at the CpG site (A) cg09892236 and (B) cg23106779 was inversely correlated with TKTL1 gene expression in melanoma samples. (PPTX 114 kb