Abstract We propose to use a systems approach that combines well-defined cohorts with unbiased large-scale profiling to elucidate signatures defining immune responsiveness in the context of divergent disease outcomes. Standardization, both at the assay and analytical levels, will allow comparisons and integration of data across projects. To maximize the immune profiles of samples generated in our Projects—and the shared analysis and interpretation of data— we propose a Single Cell Phenotyping Core to conduct and analyze multiparameter immune markers using shared platforms. The platforms of the Core include mass cytometry (CyTOF) for multiparameter single cell analysis of samples from the Research Projects (Aim 1). This new technology, which overcomes many of the limitations of fluorescence-based flow cytometry, provides unprecedented cellular analysis of multiple cell populations simultaneously and is a powerful technique for translational investigations. Our core will support seamless web interface and in depth computational analysis needs of the projects (Aim 2). In addition, we will use nanowell-based single-cell analysis for multispectral imaging cytometry (MuSIC) to measure, analyze and report the surface expression of up to 16 markers on immunocytes in sorted populations of interest or in sparse samples, including synovial fluid and EM biopsies (Aim 3). Finally, we will extend the capabilities of the nanowell platform for performing single-cell RNA-sequencing, which provides a unique and unbiased approach for resolving heterogeneous subsets of immune cells (Aim 4). Array-wide RNA- sequencing of targeted cell types or sparse samples is an innovative platform to probe the intrinsic differences between cells of interest and to refine the molecular signatures of cells implicated in disease.