RNA sequencing of control and CIP2A siRNA silenced basal-like breast cancer cell line HCC38

The purpose is to study the transcriptional changes in basal like breast cancer cell line HCC38 on depletion of CIP2A. We have used 3 unique siRNA sequences of CIP2A and 3 control samples (Mock and 2 unique non-targeting sequences) for the RNA Seq. We identified differentially expressed genes in CIP2A knockdown conditions compared to the control samples and identified pathways regulated by CIP2A in this cell line using GSEA. Overall design: CIP2A was silenced using 3 unique CIP2A siRNAs. Oligofectamine was used as the transfection reagent and standard manufacturer's protocols were followed. Non transfection control (Mock) and two nontargeting control siRNAs were used as controls.