LSEC capillarization is most prominent in zone 3, and CD34 represents LSEC capillarization more accurately than CD31. (A, B) Violin plots showing expression levels of capillarization-associated genes in LSECs (clusters 2, 3, and 4) of control and cirrhotic mice. Each dot represents a single cell. White lines indicate median expression values. (C) Immunolabeling of CD34 or CD31 in frozen liver sections from endothelial-GFP reporter mice. Red indicates CD34 or CD31 (frequently used capillarization markers), green indicates GFP (endothelial cells), blue indicates DAPI (nuclei). Scale bar: 100 μm. Images were taken using a confocal fluorescence microscope. (D, E) Expression of Kdr, Nrp1 (genes to maintain LSEC phenotype), and extracellular matrix genes in LSECs (clusters 2, 3, and 4) of control and cirrhotic mice. Each dot represents a single cell. White lines indicate median expression values. (F) Differential gene expression between control and cirrhotic mice in each cluster of LSECs (corresponding to zones 1, 2, or 3). The numbers in the figure indicate fold changes of expression levels (cirrhosis relative to control). The numbers greater than 1 (red) mean upregulation in LSECs of cirrhotic livers, while those less than 1 (blue) mean downregulation. The exact number is the magnitude of the fold change. All fold changes are statistically significant (P < .05). The hyphen (in gray cells) indicates no statistical significance between cirrhotic and control mice.