Fig. 1
Experimental setup and the effect of PHD3 silencing on 786-O proteome. a siRNA-mediated silencing of PHD3 protein level in 786-O ccRCC cell line using two individual siRNA sequences in normoxic and in hypoxic (1% O2) condition. Quantification of three biological replicates, mean ± SEM, fold change to control (Scr). Asterisk indicates a statistically significant difference (*p < 0.05, **p < 0.01). b siRNA-mediated silencing of PHD3 mRNA expression, quantification of three individual experiments. Mean ± SEM, fold change to Scr (***p < 0.001). c Flow chart of the experimental procedure. 786-O cells were transfected with siPHD3#1 or with a non-targeting control siRNA (Scr) for 24 h followed by a hypoxic (1% O2) or normoxic (21% O2) exposure. Three independent experiments were performed; proteins were extracted, followed by in-gel digestion with trypsin. Purified peptides were ran through mass spectrometer. Protein identification was done with Mascot database search. Protein quantification was carried out with Progenesis QI, followed by testing the differential expression between sample groups using peptide-level expression change averaging (PECA). d Western blot validations of selected proteins in 786-O and RCC4 cell lines with two individual siRNA sequences targeting PHD3, representative analyses are shown