UniProt Accession Number Reagent Type Target Name / Protein Biomarker Target Species Host Organism Isotype Clonality Vendor Catalog Number Conjugate RRID Availability Method Tissue Preservation Target Tissue Tissue State Detergent Antigen Retrieval Conditions Dye Inactivation Conditions Recommend Agree Disagree Contributor Notes
P16284 Primary Antibody CD31 Human Mouse IgG1 WM59 BioLegend 303133 AF700 AB_2566326 Stock IBEX2D Manual 1:4 Cytofix/Cytoperm Fixed Frozen Lymph Node NA 0.3% Triton-X-100 NA 1 mg/ml LiBH4 15 minutes Yes 0000-0003-4379-8967 [3, 1] NA 0000-0003-4379-8967  
P16284 Primary Antibody CD31 Human Mouse IgG1 C31.3+C31.7+C31.10 Novus Biologicals NBP2-47785AF700 AF700 NA Stock Multiplexed 2D Imaging FFPE Tonsil NA 0.3% Triton-X-100 pH 6 for 40 minutes at 95C (AR6 Akoya Biosciences AR600250ML) NA Yes 0000-0003-4379-8967 NA 0000-0003-4379-8967 1
P16284 Primary Antibody CD31 Human Mouse IgG1 WM59 BioLegend 303133 AF700 AB_2566326 Stock IBEX2D Manual 1:4 Cytofix/Cytoperm Fixed Frozen Lymph Node Follicular Lymphoma 0.3% Triton-X-100 NA 1 mg/ml LiBH4 15 minutes Yes 0000-0003-4379-8967 [2] NA 0000-0003-4379-8967  
P16284 Primary Antibody CD31 Human Mouse IgG1 C31.3+C31.7+C31.10 Novus Biologicals NBP2-47785AF700 AF700 NA Stock Multiplexed 2D Imaging FFPE Tonsil NA 0.3% Triton-X-100 pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond NA Yes 0000-0003-4379-8967 NA 0000-0003-4379-8967 2

Publications

  1. A. J. Radtke et al., “IBEX: an iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues”, Nat. Protoc., 17(2):378-401, 2022, doi: 10.1038/s41596-021-00644-9.

    A. J. Radtke et al., “Accompanying dataset for: IBEX: An iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues”, doi: 10.5281/zenodo.5244550.

  2. A. J. Radtke et al., “A Multi-scale, Multiomic Atlas of Human Normal and Follicular Lymphoma Lymph Nodes”, bioRxiv, 2022, doi: 10.1101/2022.06.03.494716.

  3. A. J. Radtke et al., “IBEX: A versatile multiplex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues”, Proc Natl Acad Sci, 117(52):33455–33465, 2020, doi:10.1073/pnas.2018488117

Additional Notes

  1. Labels endothelial cells in human FFPE tonsil samples based on patterning and spatial distribution in tissues. AF647 format is brighter but AF700 format can be used at a high concentration to label vessels.
  2. Labels endothelial cells in human FFPE tonsil samples based on patterning and spatial distribution in tissues. AF647 format is brighter but AF700 format can be used at a high concentration to label vessels. Dual antigen retrieval (pH 6 and 9) yields a better signal than pH 6 alone.
Human lymph node: CD31 (magenta, catalog number 303133), CD138 (blue, catalog number 356504), and IRF4 (green, catalog number 646404 )
Human lymph node: CD31 (red, catalog number 303133) and CD49a (cyan, catalog number 328303)