RNA-Seq analysis of breast cancer cells after shikonin treatment

We performed RNA-seq analysis using differnt breast cancer cell lines (MCF-7, SK-BR-3 and MDA-MB-231) after shikonin treatment. We reported that shikonin enhances the expression of DUSP-1 and DUSP-2. Shikonin induces apoptosis and decreases the phosphorylation of JNK1/2 through activationg DUSP-1 and DUSP2. Overall design: We treated three breast cancer cell lines with 10 µ? shikonin for 6 hr. The gene expression profiling was performed using RNA-seq. Numbers of significantly differentially expressed (SDE) genes in different human breast cancer cell lines under shikonin treatment had been identified. We analyzed the functional annotation and performed the pathway analysis using 38 common SDE genes.