Fig. 5

RNAseq analysis of CRISPR modified cells. A Principal component analysis based on gene expression for all samples (baseline and cisplatin-treated samples) post performing combat on samples to remove batch effect for BT-549 and T47D cell lines. B Expression of SLFN11 across baseline and cisplatin-treated samples in BT-549 and T47D cell lines. Statistical significance was assessed using an unpaired t test. C VennDiagram of common genes between BT-549 and T47D which are positively (N = 8) and negatively (N = 20) correlating with SLFN11 (correlation coefficient R <|0.5|) based on the baseline samples. Heatmap showing the expression of positively and negatively correlating genes with SLFN11 (N = 28). D VennDiagram of differentially expressed genes between BT-549 and T47D cell lines in UNISAM up (vs. control) and KRAB down (vs. control) (FDR < 0.01, logFC <|1|). Volcano plot showing upregulated DEG between UNISAM vs, control and downregulated DEG between KRAB vs, control in baseline samples (FDR < 0.01, logFC <|1| considered as significant). E VennDiagram of differentially expressed genes between BT-549 and T47D cell lines in UNISAM down (vs. control) and KRAB up (vs. control) (FDR < 0.01, logFC <|1|) in baseline samples. BT-549 CTRL and modified cells (UNISAM and KRAB) N = 6. T47D CTRL and modified cells (UNISAM and KRAB) N = 5. Cisplatin treated samples for each cell line N = 9 for all analysis performed