OMAP-7 Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Lung with Cell DIVE, v1.4

OMAP-7 was designed for Cell DIVE imaging of human formalin fixed paraffin embedded (FFPE) lung tissue. Cell DIVE<br>enables highly multiplexed single cell analysis using antibody-based imaging (Gerdes et al. 2013). The tissue slides<br>were prepared with a two-step antigen retrieval process (pH 6 and pH 9) as described (McDonough et al. 2020). Antigens<br>were detected using either primary antibodies with fluorophore-labeled secondaries or fluorescent dye conjugated<br>antibodies. The protocol can be found here (Pryhuber et al. 2022). The panel contains 30 antibodies, 4 of which are<br>used for cell segmentation (Na/K ATPase, Cytokeratin, Cadherin, and S6) and the nuclear marker DAPI for image<br>alignment and nuclear segmentation. This OMAP provides a spatial context for key cell types in the ASCT+B lung table<br>v1.1 (Pryhuber and Sun 2021). Additionally, the inclusion of protein biomarkers such as AGTR1, Cathepsin L, TMPRSS2,<br>ICAM-1, and CD55 allow characterization of proteins relevant to SARS-CoV-2 infection and profiling of the<br>renin-angiotensin system (RAS) that may play a role in COVID-19 disease. The core and essential protein biomarkers<br>detailed here overlap (~25%) with the panel developed for multiplexed imaging of lung samples established using<br>conventional automated IHC staining for FFPE material. This OMAP does not contain antibodies for typing subsets of<br>fibroblasts, macrophages, or endothelial cells. A representative dataset using this OMAP can be found here: (Surrette<br>et al. 2023). This revised v1.4 OMAP corrects CD3D to CD3E.<br><br>**Bibliography:**<br><br>* Gerdes, Michael J., Christopher J. Sevinsky, Anup Sood, Sudeshna Adak, Musodiq O. Bello, Alexander Bordwell, Ali Can, et al. 2013. “Highly Multiplexed Single-Cell Analysis of Formalin-Fixed, Paraffin-Embedded Cancer Tissue.” *Proceedings of the National Academy of Sciences* 110 (29): 11982–87. https://doi.org/10.1073/pnas.1300136110.<br>* McDonough, Liz, Chrystal Chadwick, Fiona Ginty, Christine Surrette, and Anup Sood. 2020. “Cell DIVE™ Platform | Slide Clearing and Antigen Retrieval.” December. https://doi.org/10.17504/protocols.io.bpwumpew.<br>* Pryhuber, Gloria, Gail Deutsch, Christine Surrette, Lisa Lowery, Heidie Huyck, and Cory Poole. 2022. “HuBMAP | GE/URMC/SCH Cell DIVE™ Modality Overview.” February. https://doi.org/10.17504/protocols.io.b4kgqutw.<br>* Pryhuber, Gloria, and Xin Sun. 2021. “Lung (v1.1) Graph Data, v1.1.” https://lod.humanatlas.io/asct-b/lung/v1.1/.<br>* Surrette, Christine, Lisa Lowery, Gail Deutsch, Gloria S. Pryhuber, and Fiona Ginty. 2023. “Multiplexed Immunofluorescence Staining Dataset - OMAP 7 - Lung, Cell DIVE.” Zenodo. https://zenodo.org/records/7731162.