Table 2.

Table summary of usage, advantages, and disadvantages of relevant technologies for HDAC studies.

Technology	Primary Usage	Advantages	Disadvantages
Chromatin immunoprecipitation sequencing (ChIP-seq)	Epigenomics	Quantifies histone and other DNA-binding protein’s location on genome	High cost; reliance on highly sensitive and selective antibody
Single cell RNA sequencing (scRNA-seq)	Transcriptomics	Measures differentially expressed genes (e.g., response to HDACIs) in a variety of cell types	Poor cell quality control can lead to low-resolution results and inconsistent transcript coverage
Liquid chromatography-mass spectrometry (LC-MS)	Proteomics	Identifies residues of interest in post-translational modifications	High cost, sensitive to noise and it is not genome-scale unlike transcriptomics
13C Magnetic Resonance Spectroscopic Imaging (13C-MRSI)	Metabolomics	Selectable, tracer metabolites of interest; minimally invasive in vivo	Expensive to achieve the resolution required for measuring metabolic shifts