138 CHAPTER 5 Figure 3. Benchmark of molecular profile preservation of normal liver biopsies from patients with cancer. Molecular profile preservation benchmark of snap freezer vs liquid nitrogen. A. Unsupervised cluster analysis of the phosphoproteome of liver tissue samples of four individual patients shows that patient-specific profiles can clearly be identified in samples snap frozen in the snap freezer as well as in liquid nitrogen. Color key indicates Z-scores. B. Unsupervised cluster analysis of RNA expression of 100 most variable genes shows that 3 individual patient profiles can be clearly identified using samples processed in both freezing methods. Color key indicates Z-scores. EFFECT OF DIFFERENT FREEZING RATES ON PHOSPHOPROTEOMIC PROFILES Three types of vials with different thermal conduction properties (polypropylene, aluminum and aluminum vials covered in paper tape) and two coolants (LN2 and pre-cooled isopentane) were used to determine differences in freezing rate of HCT116 cancer cell lines samples to reach -80 °C8 (Supplementary Figure 2). Polypropylene vials immersed in LN2 versus pre-cooled isopentane had a mean freezing time of 2 versus 25 seconds (s), respectively, while aluminum vials without paper tape covering had freezing times of 4 s in LN2 and 10 s in isopentane (Table 2). To study whether changes to the phosphoproteome would be detectable in samples from
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