Project Summary Single-cell genome-wide profiling enabled by next-generation sequencing (NGS) has been fundamentally changing how molecular biology is studied. Cells are basic unit of life and profiling each individual cell provides the most accurate and precise characterization of tissue samples that likely contain numerous diverse cell types and subpopulations. In this project, we will develop high-throughput and high-quality single-cell technologies based on droplet microfluidics for mapping genome-wide histone modifications and conducting multi-omic profiling that integrates epigenomic and transcriptomic analyses. Our single-cell ChIP-seq and multi- omic technology will allow massive number of cells to be examined rapidly. Furthermore, by using drastically simplified molecular biology and microfluidic technology, our scChIP-seq will produce significantly improved genome coverage. Our multi-omic profiling will allow integrative analysis of epigenomic and transcriptomic features and establishment of correlations between gene regulation and expression for precise understanding of cell type, fate and potential at the single cell level. As a proof-of-principle, we will apply these technologies to examine the effects of psychedelic drug on mouse brain biology. Brain is the most complex organ that exhibit enormous heterogeneity and complexity in terms of the cell types and subpopulations involved and studies of brain neuroscience will benefit from the single-cell approach tremendously. By the end of this 4-year project, we will push these technologies to maturity for tissue-based studies with real biomedical relevance.