The main goal of this core is to establish and provide robust experimental procedures for profiling the transcriptomes and proteomes of immune cells. We will provide innovative methods for molecular profiling in bulk populations in the context of perturbations and at the single cell level for all of the proposed projects including single cell RNA-Seq and mass cytometry by time-of-flight (CyTOF) for profiling single cell proteomes and signaling. Projects in the Center demand population-level RNA-Seq on a relatively large-scale and involve immune cell profiling for various tissue sites, in the context of different viral infections and perturbations, and at different time points during perturbation experiments. To address these needs, the core will provide a novel implementation of highly multiplexed RNA-Seq that allows large-scale, inexpensive expression profiling in an automated, multi-well plate format. Single cell RNA-Seq and CyTOF are unique in their abilities to reveal phenotypic heterogeneity among apparently homogeneous populations of cells. These capabilities are essential for studying the dynamics of immune cells, which do not respond uniformly to perturbations and may exhibit tissue-dependent phenotypes. Combining single cell RNA-Seq and CyTOF will reveal not only the transcriptional heterogeneity underlying immune cell populations, but also protein markers and post- translational modifications of signaling molecules like phosphorylation.