Extended Data Fig. 6: Characterization of macrophages in mouse liver fibrosis.
From: Resolving the fibrotic niche of human liver cirrhosis at single-cell level
a, Clustering and annotating 3,250 mouse (m)MPs from healthy (n = 3) and fibrotic (4 weeks CCl4 treatment; n = 3) livers. b, Annotating mouse MP cells by injury condition. c, Heat map of mouse MP cluster marker genes (top; colour-coded by cluster and condition), with exemplar genes labelled (right). Columns denote cells; rows denote genes. d, Selected genes expressed in 3,250 mouse MPs. e, Representative flow cytometry plots of the gating strategy (n = 8 from two independent experiments) for identifying mouse KCs, CD9− TMs and CD9+ SAMacs in fibrotic mice. f, Quantifying mouse macrophage subpopulations by flow cytometry in healthy (n = 6) and fibrotic (n = 8) mouse livers from two independent experiments. The macrophage subpopulation (x axis) is shown as a percentage of total viable CD45+ cells (y axis). Data are mean ± s.e.m. P values determined by two-tailed Mann–Whitney test. g, Co-culture of primary mouse HSCs from uninjured livers and either FACS-isolated CD9− mouse TMs or CD9+ mouse SAMacs from fibrotic livers (n = 8 mice; two independent experiments). Right, qPCR of Col3a1 expression in HSCs; expression relative to mean expression of quiescent HSC. P value determined by two-tailed Wilcoxon test. h, Clustering 3,250 mouse MPs and 10,737 human (h)MPs into five clusters using canonical correlation analysis. Annotation of cross-species clusters (identity). i, Annotation of human and mouse macrophage subpopulations from 3,250 mouse MPs and 10,737 human MPs. j, Selected genes expressed in 3,250 mouse MPs and 10,737 human MPs.
