RNA sequencing (RNA-seq) and transcriptome data analysis
The WT cells were treated with Bazhen decoction (control, low dose
(10μg/mL), high dose (100μg/mL)) for 24hr. The cells were harvested and
sent to perform RNA-seq by commercial service. For each sample, 20G of
RNA-seq data were collected for further analysis.
The single sample gene set enrichment analysis (ssGSEA) [34] was
performed to analyze the RNA-seq to get the scores for signaling
pathways. The C2 and C5 gene sets from Molecular Signatures database
[35] were used as the pathway database for ssGSEA analysis. The top
differential regulated pathways were plotted with Morpheus
(https://software.broadinstitute.org/morpheus) to obtain the
transcriptome profile regulated by Bazhen decoction.