OMAP-29 Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of human mouth mucosa with CODEX, v1.0

OMAP-29 was designed for CO-Detection by indEXing (CODEX) imaging of human formalin fixed paraffin embedded (FFPE)<br>oral mucosa samples using the Akoya Biosciences PhenoCycler-Fusion (PCF) platform (Black et al. 2021). Tissues were<br>fixed using 4% paraformaldehyde (PFA) instead of the more common 10% formalin prior to paraffin embedding. A two-step<br>antigen retrieval process at pH 9 was used, as detailed in Houston 2024. Antigen detection was achieved using primary<br>antibodies conjugated with fluorophore-labeled barcodes, following the methodology outlined in Easter et al. 2024. The<br>antibody panel includes 40 antibodies and the nuclear marker DAPI, which supports both image registration and nuclear<br>segmentation. This OMAP provides spatial context for most anatomical structures and cell types represented in the<br>ASCT+B mouth table v1. It includes key marker antibodies for major oral mucosa cell populations: epithelial cells<br>(pan-cytokeratin), fibroblasts (vimentin), immune cells (CD45), and vascular cells (CD31). The panel enables detailed<br>mapping of structural and immune microenvironments of the oral mucosa in FFPE samples.<br><br>**Bibliography:**<br><br>* Black, Sarah, Darci Phillips, John W. Hickey, Julia Kennedy-Darling, Vishal G. Venkataraaman, Nikolay Samusik, Yury Goltsev, Christian M. Schürch, and Garry P. Nolan. 2021. “CODEX Multiplexed Tissue Imaging with DNA-Conjugated Antibodies.” *Nature Protocols* 16 (8): 3802–35. https://doi.org/10.1038/s41596-021-00556-8.<br>* Easter, Quinn T., Bruno Fernandes Matuck, Germán Beldorati Stark, Catherine L. Worth, Alexander V. Predeus, Brayon Fremin, Khoa Huynh, et al. 2024. “Single-Cell and Spatially Resolved Interactomics of Tooth-Associated Keratinocytes in Periodontitis.” *Nature Communications* 15 (1): 5016. https://doi.org/10.1038/s41467-024-49037-y.<br>* Houston, Andrew. 2024. “Akoya Biosciences PhenoCycler Fusion (Formerly CODEX) User Guide,” January. https://www.protocols.io/view/akoya-biosciences-phenocycler-fusion-formerly-code-c7fszjne.