Bulk and single cell profiling of the transcriptional response to Trichostatin A and Valproic Acid using CAGE

To better understand the transcriptomic changes that occur in response to HDACi treatment, we perform CAGE on dermal fibroblasts, HepG2, and MCF7 cells after TSA or VPA treatment, at both bulk and single cell level. We make detailed annotation of the identified coding and noncoding RNA transcription start sites and enhancers, in addition to their expression levels. Overall, 3 cell types are subjected to 3 different treatments, including control, TSA, and VPA. For bulk CAGE, 3 replicates of each cell type x treatment were made. For C1 CAGE,