Fig. 2

Validation of shRNA candidate genes by siRNAs in six ovarian cancer cell lines a siRNA screens are done in three serous (S) and three non-serous (NS) cell lines. p53 status is indicated; Ovcar3 (Mut: P72R, R248Q), Ovcar8 (Mut: amino acid deletion: aa126-132), Igrov1 (Mut: Y126C), Ovcar5 and Skov3 (Null, no p53 detected on Western blot), A2780 (wide type) [6]. The value of each siRNA from CellTiter Glo assay was normalized by the average value of siNeg in each plate to calculate relative cellular viability, and then the average of three normalized values were plotted with standard deviation. The red bar is drawn at 1.0 which means no toxicity upon knockdown. Cellular viability for each siRNA construct across the six cell lines was compared to that with siNeg; * indicates p < 0.05 (Mann Whitney U-test). Error bars represent the standard error of the mean for each cell line, per siRNA. b Target shRNA depletion (shown as fold change: FC) at two different time points compared to day 0 (baseline control) are shown. shRNA screens were done in four biological replicates in Ovcar5 and A2780, and in six biological replicates in Ovcar3 and Igrov1 [6, 7]. p-value compares the log of the estimated normalized averages between experiments (see methods). c Genetic alterations of six candidate targets were examined in TCGA ovarian tumor samples with sequencing and CNA data using a web-based cBioPortal tool (http://www.cbioportal.org/public-portal/). d Overall survival analysis based on the alterations of six candidate targets in OC was extracted from TCGA data analysis