OMAP-9: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Kidney with CODEX, v1.4

OMAP-9 was designed for CO-Detection by indEXing (CODEX) imaging of fresh frozen human kidney tissue using the<br>protocol described by Sabo et al. (2023a). The panel includes 41 antibodies and the nuclear marker DAPI for image<br>alignment and nuclear segmentation. OMAP-9 provides a spatial context for all anatomical structures and most cell<br>types present in the ASCT+B kidney table v1.1. This OMAP expands upon OMAP-3 (Neumann and Farrow 2024), which used an<br>18-plex CODEX panel, by incorporating additional markers that enable granular phenotyping of key kidney cells. These<br>include structural cells (e.g., Podocalyxin, LRP2, E-cadherin, SLC12A3, Na/K ATPase, Cytokeratin 8), T cells (e.g.,<br>CD3D, CD4, CD45RO, CD8, FOXP3, GATA-3), myeloid cells (e.g., CD11c, CD68, CD206, HLA-DR, Myeloperoxidase), and B cells<br>(CD20). Antibodies against injury-related markers (e.g., KIM1, IGFBP7, Osteopontin, PLSCR1, VCAM1, MCP1,<br>phospho-c-JUN, phospho-MLKL, Fibronectin, Collagen IV, LC3, Cystatin 3, PROM1) support profiling of disease<br>progression and tissue repair. Antibody clones for vimentin, beta-catenin, and uromodulin differ from those in OMAP-3.<br>Mesangial cells in the glomerulus are not targeted due to the lack of suitable CODEX-compatible antibodies. Additional<br>details on tissue preparation and the CODEX multiplexing workflow are provided by Sabo et al. (2023b). OMAP-9 v1.1<br>corrects author names, and v1.5 updates the UniProt accession number for CD45RO to P08575-4, differentiating it from<br>CD45. A representative dataset is available via Barwinska, Sabo, and EL-Achkar (2024).<br><br>**Bibliography:**<br><br>* Barwinska, Daria, Angela Sabo, and Tarek EL-Achkar. 2024. “OMAP-9.” Zenodo. https://doi.org/10.5281/zenodo.14537009.<br>* Neumann, Elizabeth K., and Melissa Farrow. 2024. “3-Kidney-Codex (v1.3) Graph Data, v1.3.” https://lod.humanatlas.io/omap/3-kidney-codex/v1.3/.<br>* Sabo, Angela R., Connor J. Gulbronson, Daria Barwinska, Michael J. Ferkowicz, William Bowen, Seth Winfree, and Tarek Ashkar. 2023a. “Indiana University Adapted Akoya Phenocycler-Fusion Tissue Staining and Imaging Protocol for Fresh Frozen Kidney Tissue,” March. https://www.protocols.io/view/indiana-university-adapted-akoya-phenocycler-fusio-cpchvit6.<br>* Sabo, Angela R., Connor J. Gulbronson, Daria Barwinska, Michael J. Ferkowicz, William Bowen, Seth Winfree, and Tarek Ashkar. 2023b. “Indiana University Adapted Akoya Phenocycler-Fusion Tissue Staining and Imaging Protocol for Fresh Frozen Kidney Tissue,” March. https://www.protocols.io/view/indiana-university-adapted-akoya-phenocycler-fusio-cpchvit6.