Fig 1: Combination of CITE-seq, scRNA-seq, snRNA-seq, and spatial analyses enables identification of all hepatic cell types including bona fide cell doublets, related to Figure 1(A and B) Top DEGs (A) and DEPs (B) for cell types from Figure 1B.(C) Distinct profiles of cells or nuclei within the UMAP depending on isolation protocols; 71,162 cells from ex vivo digestions, 96,066 cells from in vivo digestions, and 18,666 nuclei. Numbers on plots represent numbers of cells/nuclei per population.(D) Correlation plots showing genes captured within the KC, B cell and neutrophil populations with and without addition of CITE-seq antibodies.(E) Expression of VSIG4, CD206, and ESAM (protein, top) and Vsig4, Mrc1, and Esam (mRNA, bottom).(F) UMAP showing clusters of cells when only minimal QC for gene number and % mitochondrial genes is performed; 17,669 cells pooled from 3 samples. Expression of Cd5l, Cd19, and Kdr by the clusters facilitating identification of cell types per annotation.(G) CITE-seq data from (F) in Flow-Jo showing expression of CD206 and ESAM in total KCs (left) and total B cells (middle). Numbers represent % of entire KC or B cell population. Identified populations were then mapped back onto the original UMAP (right).(H) Expression of CD31, CD26, and CD38 by indicated populations.(I) Heatmaps showing expression of top DEGs between KC1s and LSECs (left), KC2s and KC1s + LSECs (middle) and B cell2s and B cell1s + LSECs (right).(J) 3D reconstruction of murine liver following perfusion with antigen fix to inflate endothelial cells and staining with antibodies against CD31, CD206, and F4/80.(K) UMAP showing clusters generated from Visium analysis of liver tissue (4 samples) and liver capsule (1 sample).(L) Top unbiased genes defining zonation trajectory from portal to central vein in Visium.(M) Expression of Glul and Epcam by confocal microscopy (left), annotation of portal, periportal, mid, and central regions on same tissue section (middle) and overlay of both datasets (right).(N) Identification of cholangiocyte (left) and cDC (right) signatures on zonated Visium spots.(P) Molecular Cartography showing expression of indicated zonated hepatocyte mRNAs in liver tissue. Data are representative of 2 mice.(O) Expression of Itgae (encoding CD103) in the UMAP of the total liver (left) and flow cytometric analysis of total cDC1s for CD103 and MHCII expression in the healthy murine liver (right).