Fig 2: Expected outcome of a bioinformatic unbiased analysis of the 16-color murine myeloid flow cytometry panel(A) Single alive CD45+ CD3- CD19- cells were subjected to bioinformatic FlowSOM analysis based on expression of Ly6G, Ly6C, PDCA1, CD11b, CD11c, F4/80, MHCII, CD172a, CD24, XCR1, and CD4 with a metacluster number of 40. User-determined thresholds for positive signal were applied to all features. The analysis identified 40 distinct clusters of cells.(B) Clusters were annotated based on key myeloid lineage features.

Fig 3: A proteogenomic atlas of the healthy murine liver(A) Hepatic cells were isolated from healthy C57B/l6 mice by ex vivo (5 mice, 15 samples) or in vivo (5 mice, 19 samples) enzymatic digestion. Alternatively, nuclei were isolated by tissue homogenization (4 mice, 12 samples). Live cells/intact nuclei were FACS-purified. For cells, total live, live CD45+, live CD45−, live hepatocytes, or myeloid cells (live CD45+, CD3−, CD19−, B220−, NK1.1−) were sorted. 18 samples (7 ex vivo, 11 in vivo) were also stained with a panel of 107–161 barcode-labeled antibodies for CITE-seq analysis. All datasets were pooled together and after QC 185,894 cells/nuclei were clustered using TotalVI.(B) UMAP of sc/snRNA-seq data.(C) Tissue and capsule images from Visium analysis with clusters overlaid.(D) UMAP of zonation of Visium spots (left) and origin of the cells (right).(E) Zonation pattern mapped onto tissue slice.(F and G) Indicated cell signatures from sc/snRNA-seq mapped onto the Visium zonation data.(H) mRNA zonation pattern in Visium highly multiplexed protein analysis and VSIG4-ADT expression pattern (left) and zonated expression patterns of indicated antibodies (right).(I) MICS analysis of indicated proteins.(J) Molecular Cartography of indicated genes and cell types.(K) mRNA (Xcr1, Flt3l, Mafb, and Clec10a) and protein (MHCII and F4/80) expression in the same tissue slice. Scale bars, 50 μm. PV, portal vein; CV, central vein. Arrows indicate specific cell types, colors correspond to cell type/markers. Images are representative of 2–4 mice. See also Figure S2 and Tables S1, S2, S3, and S5.