ArticleEuropean journal of immunology2021
Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction.
Article in European journal of immunology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed, 101 citations in OpenAlex.
- Immune cell topography predicts response to PD-1 blockade in cutaneous T cell lymphoma.Nature communications · 2021Trial
- Near-infrared photochromic miniprotein enables photoacoustic molecular imaging of acute inflammation and intracellular antigens.Nature methods · 2026Article
- ARCADIA reveals spatially dependent transcriptional programs through integration of scRNA-seq and spatial proteomics.Bioinformatics (Oxford, England) · 2026Article
- Spatium: A Protein Language Foundation Model for Spatial Proteomics.bioRxiv : the preprint server for biology · 2026Article
- Investigating Spatial Dynamics in Spatial Omics Data with StarTrail.Journal of the American Statistical Association · 2026Article
- Subcellular localization as a driver of protein function.Nature reviews. Molecular cell biology · 2026Review
- Single-cell spatial pharmacobiology identifies conserved stromal barriers to therapeutic antibody delivery in human solid tumors.Nature biotechnology · 2026Article
- Cycle-consistent deep generative modeling unifies cellular states across unpaired spatial and single-cell modalities.bioRxiv : the preprint server for biology · 2026Article
- Robust integration of single-cell datasets with imbalanced modality composition.Nature communications · 2026Article
- Single-cell data integration across weakly linked modalities.PLoS computational biology · 2026Article
- Single-Cell Protein Assays in Context: From 2D to 3D and In Situ Analysis.Annual review of analytical chemistry (Palo Alto, Calif.) · 2026Review
- The Evolution of Spatial Omics Technologies Introduces A Novel Avenue for Lung Cancer Research.Genomics, proteomics & bioinformatics · 2026Review
- Genomic and transcriptomic analyses of melanoma in Japanese patients reveal candidate biomarkers for immune checkpoint inhibitor responders.Communications medicine · 2026Article
- Comparative Evaluation of Antibody-Oligonucleotide Conjugation Strategies for Multiplexed Imaging Applications.Laboratory investigation; a journal of technical methods and pathology · 2026Article
- Current Methods in CODEX High-Multiplex Microscopy to Describe Spatial Relationships in the Tissue Microenvironment.Methods in molecular biology (Clifton, N.J.) · 2026Article
- ST-FFPE-mIF: integrating spatial transcriptomics and multiplex immunofluorescence in formalin-fixed paraffin-embedded tissues using Stereo-seq.Genome biology · 2025Article
- SPACEc: a streamlined, interactive Python workflow for multiplexed image processing and analysis.Nature communications · 2025Article
- CelLink: integrating single-cell multi-omics data with weak feature linkage and imbalanced cell populations.Nucleic acids research · 2025Article
- ARCADIA Reveals Spatially Dependent Transcriptional Programs through Integration of scRNA-seq and Spatial Proteomics.bioRxiv : the preprint server for biology · 2025Article
- Concerted changes in Epithelium and Stroma: a multi-scale, multi-omics analysis of progression from Barrett's Esophagus to adenocarcinoma.Developmental cell · 2025Article
11 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 3 institutions in 2 countries.
Funding
Abstract
Multiparameter tissue imaging enables analysis of cell-cell interactions in situ, the cellular basis for tissue structure, and novel cell types that are spatially restricted, giving clues to biological mechanisms behind tissue homeostasis and disease. Here, we streamlined and simplified the multiplexed imaging method CO-Detection by indEXing (CODEX) by validating 58 unique oligonucleotide barcodes that can be conjugated to antibodies. We showed that barcoded antibodies retained their specificity for staining cognate targets in human tissue. Antibodies were visualized one at a time by adding a fluorescently labeled oligonucleotide complementary to oligonucleotide barcode, imaging, stripping, and repeating this cycle. With this we developed a panel of 46 antibodies that was used to stain five human lymphoid tissues: three tonsils, a spleen, and a LN. To analyze the data produced, an image processing and analysis pipeline was developed that enabled single-cell analysis on the data, including unsupervised clustering, that revealed 31 cell types across all tissues. We compared cell-type compositions within and directly surrounding follicles from the different lymphoid organs and evaluated cell-cell density correlations. This sequential oligonucleotide exchange technique enables a facile imaging of tissues that leverages pre-existing imaging infrastructure to decrease the barriers to broad use of multiplexed imaging.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.