Core C has two overarching goals: (1) to provide reliable and technically consistent complex murine models of lung transplantation to identify pathways causally linked to primary graft dysfunction (PGD) and chronic lung allograft dysfunction (CLAD); (2) to provide the Project investigators expertise with established and emerging technology platforms for advanced phenotyping of mice and human tissues after lung transplantation. All four Projects will use these tools to test and validate their hypotheses. Because the technologies deployed by Core C generate unbiased data that can inform multiple studies, Core C will work with Core A to make this resource available to all PPG investigators and the research community. Achieving these goals will provide the PPG investigators with (1) quantitative insights into the molecular pathways that underlie the development of PGD and CLAD, (2) pathways that drive the enhanced incidence of allograft dysfunction in the presence of clinical risk factors, and (3) measurements of the response to current therapeutic strategies as well as novel, validated protein targets for therapeutic intervention. Accordingly, the Cell Phenotyping and Mouse core (Core C) will support all four scientific projects by focusing on the following specific aims: Aim 1: Provide well-characterized murine models of murine orthotopic lung transplant and live cell imaging of immune infiltration into the allograft. Core C investigators have published extensively using murine lung transplant PGD models and chronic lung allograft dysfunction. Core C measures of PaO2/FIO2 ratio, flow cytometry assessment of lung inflammatory cell populations, lung fibrosis measurements, murine pulse oximetry, and in vivo live imaging through a surgically placed window to accurately phenotype these models. Aim 2. Provide a multi-omic assessment of lung injury and fibrosis after lung transplantation using homologous approaches to those used in humans. Core C investigators have developed protocols to process lung tissue for various techniques that would undergo multi-omic bioinformatics analyses by Core B. These techniques include flow cytometry, single-cell RNA- seq/CITE seq, microbiome analysis, TCR profiling, whole genome DNA methylation assays, proteomics, and metabolomics. Core C will collaborate with Core C for the sequencing and bioinformatics analyses of murine tissues processed by Core C. Aim 3: Perform breeding and genotyping of all the murine strains, including the generation of tissue- and cell-type-specific knockout and reporter animals required by the Project Investigators. Core C will breed wild-type and genetically engineered mice, including global knockouts, conditional knockouts, and transgenic and overexpressing mice, to generate inducible cell-type- and tissue-specific knockout or overexpressing mice. Core C will maintain a centralized database of all animals and perform strategic planning according to experimental plans proposed by individual Proj...