OMAP-2 Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Intestines with CODEX, v1.6

OMAP-2 was designed for CODEX (CO Detection by indEXing) imaging of fresh frozen human intestine (Black et al. 2021;<br>Kennedy‐Darling et al. 2021). The panel contains 54 antibodies and the nuclear marker Hoechst for image alignment and<br>nuclear segmentation. This panel provides spatial context for all anatomical structures and most cell types present in<br>the ASCT+B intestine table, v1.1 (Longacre, Hickey, and Lin 2021). However, this panel does not include a marker for<br>tuft cells, M cells, and subsets of major cell types that are known to be present in the intestine (e.g.,<br>neuroendocrine cell lineages, distinctions between alpha/beta and gamma/delta T cells, and IgA+ plasma cells). In<br>general, the panel was aimed to provide a broad representation of cell types found in the intestine spanning stromal,<br>immune, and epithelial origins and may be used across disease settings of the intestine. Data from this panel has been<br>analyzed as described previously (J. W. Hickey et al. 2021; 2023). All antibodies are custom conjugated in house with<br>oligonucleotide barcodes (no lot number available) and run using CODEX imaging per previous protocols (Black et al.<br>2021). Representative datasets using this OMAP can be found here (J. Hickey 2023a; 2023b). OMAP-2 v1.3 corrects the<br>RRID listed for CDX2 to AB_2864405 and the protein target detected by panCytokeratin (cloneID AE-1/AE-3, BioLegend,<br>catalog #: 914204) from KRT17 to the following: KRT1, KRT2, KRT3, KRT4, KRT5, KRT7, KRT8, KRT10, KRT14, KRT15, KRT16,<br>and KRT19. OMAP-2 v1.5 revises the UniProt accession number for CD45RO to P08575-4 to distinguish it from CD45.<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>* Hickey, John. 2023a. “Human Intestine Processed CODEX Multiplexed Images for Donors B004-6, B008 (Part 1/2).” *Dryad*. https://doi.org/10.5061/DRYAD.76HDR7T1P.<br>* Hickey, John. 2023b. “Human Intestine Processed CODEX Multiplexed Images for Donors B009-B012 (Part 2/2).” *Dryad*. https://doi.org/10.5061/DRYAD.GMSBCC2SQ.<br>* Hickey, John W., Winston R. Becker, Stephanie A. Nevins, Aaron Horning, Almudena Espin Perez, Chenchen Zhu, Bokai Zhu, et al. 2023. “Organization of the Human Intestine at Single-Cell Resolution.” *Nature* 619 (7970): 572–84. https://doi.org/10.1038/s41586-023-05915-x.<br>* Hickey, John W., Yuqi Tan, Garry P. Nolan, and Yury Goltsev. 2021. “Strategies for Accurate Cell Type Identification in CODEX Multiplexed Imaging Data.” *Frontiers in Immunology* 12 (August): 727626. https://doi.org/10.3389/fimmu.2021.727626.<br>* Kennedy‐Darling, Julia, Salil S. Bhate, John W. Hickey, Sarah Black, Graham L. Barlow, Gustavo Vazquez, Vishal G. Venkataraaman, et al. 2021. “Highly Multiplexed Tissue Imaging Using Repeated Oligonucleotide Exchange Reaction.” *European Journal of Immunology* 51 (5): 1262–77. https://doi.org/10.1002/eji.202048891.<br>* Longacre, Teri, John Hickey, and Yiing Lin. 2021. “Large-Intestine (v1.1) Graph Data, v1.1.” https://lod.humanatlas.io/asct-b/large-intestine/v1.1/.