RNA-seq based transcriptome profiling of Carpesium cernuum extract (CCE) treated MDA-MB-231 cell lines

To understand the molecular mechanism of CCE, we performed the RNA-seq analysis. Cells were seeded at 5x10^5 cells/well in 6-well plates then treated with 1μg/mL CCE for 24 h. MDA-MB-231 cells were harvested, and RNA was isolated with TRIzol. The libraries were constructed by using the Quick cDNA Library Preparation Kit and sequenced on an XTEN sequencing system. RNA-seq data were mapped to the reference genome (hg19) by using HISAT2. The reads were counted, and StringTie was used to calculate the FPKM value of the genes. The differentially expressed genes (DEGs) were identified by comparing the experimental group with the control group. mRNA profiles of control group and CCE group were generated by RNA sequencing.