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bioRxiv · 10.64898/2025.12.19.695385

Addressing complex autofluorescence signatures in solid tissue samples to enhance full spectrum flow cytometry of non-immune cells.

Gkantsinikoudi, C.·Terranova-Barberio, M.·Dufton, N. P.
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Abstract

FSFC is an emerging technology that can greatly enhance our understanding of the single-cell proteomic landscape. However, its application to cells derived from solid tissues has been hampered by their complex autofluorescence signatures and lack of optimized tools for non-immune cells. Here, we present a protocol and discuss key controls that minimize the impact of unmixing errors enabling us to resolve multiple EC subpopulations isolated from different tissues in models of chronic tissue injury. Research Topic(s)Vascular biology, cell heterogeneity, full spectrum flow cytometry Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/695385v2_ufig1.gif" ALT="Figure 1000"> View larger version (43K): org.highwire.dtl.DTLVardef@1745181org.highwire.dtl.DTLVardef@1930db9org.highwire.dtl.DTLVardef@16a0b3dorg.highwire.dtl.DTLVardef@107ec29_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsOptimisation of a FSFC panel to enable in-depth phenotyping of tissue- and model-specific endothelial subpopulations from solid tissues. Discussion of appropriate controls to minimize the impact of tissue autofluorescence and enhance the signal-to-noise ratio for cell phenotyping in complex models of inflammation and fibrosis. Trajectory analysis to track cellular plasticity over time. Application of full spectrum cell sorting to isolate rare endothelial subpopulations with complex phenotypes.

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Gkantsinikoudi, C., Terranova-Barberio, M., Dufton, N. P.. 2025-12-22. Addressing complex autofluorescence signatures in solid tissue samples to enhance full spectrum flow cytometry of non-immune cells.. https://doi.org/10.64898/2025.12.19.695385

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