Research Summary Assays to Define the Impact of Multiplexed Perturbation and Spatial Context on Gene Regulation within Single Cells Cells rewire gene expression in response to numerous environmental, developmental and therapeutic stimuli, and specific responses vary greatly among individual cell types. Such genomic reprogramming is established through DNA-binding transcription factors (TFs), which direct a dynamic system of changes to the state of chromatin near promoters and enhancers (Takahashi and Yamanaka 2016). However, measuring and interpreting such genomic choreography remains extremely challenging in heterogeneous cell populations or tissue samples. To address this issue, I describe a novel approach for multiplexed, combinatorial indexing-based, single cell ATAC-seq (sciPlex-ATAC), which enables the simultaneous profiling of the accessible genome within thousands of individual cells from virtually unlimited experimental conditions. I propose sciPlex-ATAC as a novel and informative platform for characterizing perturbations of the chromatin landscape in high-throughput chemical screens. Using this platform I plan to investigate targeted disruption of allogeneic immune stimulation in human mixed lymphocyte reactions. Finally, by adapting the nuclear labeling principles of sciPlex-ATAC, I envision “chromatin histology” as a method to resolve the spatial locations of single cell chromatin profiles within tissues.