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Table S1. Quantitative data of immunostaining (Immunohistochemistry).

Table S2. UroVysion FISH results on transitional cell carcinoma paraffin-embedded tissue sections and on cultured cancer stem-like cells from the same sample.

Table S3. Data summary of this study.

Fig. S1. Oct-4 protein expression on paraffin embedded tumor sections. (A–C) Patient 050CR07: note the random spatial distribution of positive nuclei. (D) Atypical ectopic localization of Oct-4 in a tumor section of patient 039CR07 otherwise negative for this marker. The inserts show: an enlargement of the positive nucleus (bottom left); an Oct-4 positive cell (top right) isolated from the same tumor (85% of cultured cells were positive). (E) Oct-4 expression on tumor section of patient 034CR07. (F) Oct-4 expression in human seminoma (as positive control for Oct4). Scale lines: 10 μm.

Fig. S2. Differential expression of cytokeratins in two samples of transitional cell carcinoma with different histological grade. (A,B) Expression of CK5 (A) and CK8 (B) in two consecutive sections of a high grade non-infiltrating tumor (034CR07). Note the restricted positive but mutually exclusive area for both markers. (C,D) Expression of CK5 (C) and CK8 (D) on low grade non-infiltrating tumor sections (039CR07). Scale lines: 5 μm.

Fig. S3. Graphic summary of UroVysion FISH results reported in Table SII. For each probe, values show the difference between the total number of signals recorded after culture and that of fresh tissue. Data were divided according to loss (number of signals/cell <2), disomy (number of signals/cell =2), and gain (number of signals/cell ≥3). HGIN, high grade infiltrating; HGNI, high grade non-infiltrating; LGIN, low grade infiltrating; LGNI, low grade non-infiltrating.

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