Tissue processing and antibody staining was performed as described in detail in (21 (link)). In short, 5-μm cryosections of fresh frozen lungs were fixed (Image-iT Fixative Solution, Thermo Fisher Scientific) and stained with the antibody panel listed in Table 3 and Cell-ID Intercalator-Ir (Fluidigm). Scanning of the (dried) slides was done with the Hyperion Imaging Mass Cytometer (Fluidigm). Images are available at the Figshare repository https://doi.org/10.25418/crick.19590259 .
Image processing was performed with the previously described 1-pixel expansion single-cell segmentation pipeline using imcyto (nf-core/imcyto). The resulting single-cell data were clustered with Phenograph and subsequently annotated to the different cell types (table S1).
Image processing was performed with the previously described 1-pixel expansion single-cell segmentation pipeline using imcyto (nf-core/imcyto). The resulting single-cell data were clustered with Phenograph and subsequently annotated to the different cell types (table S1).
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