Extended Data Fig. 10: The portal area in the old liver is a patchwork of normal tissue and inflammatory and strongly fibrotic niches, each of which is inhabited by a specific fibroblast subtype.
a, Schematic depiction of the Visium processing. b, Visium spot annotation. Left, Zonation information of Visium spots obtained from the original data (GSE192742)74. Right, Scores of cell types that are enriched in FiNi-seq. c, Zonation distribution of the indicated EC subtypes (top), mesenchymal cells (middle), and monocytes and macrophages (bottom). The data are presented as mean ± 95% c.i. d, Heatmap hierarchical clustering of the portal-zone spots between the deconvoluted cell types (black letters) and the MsigDB HallMark77 pathway scores (purple letters). e, Classification of portal spots by clusters obtained from (d). f, DEG analysis between portal spots of different classification. Left, Inflammatory versus homeostatic. Right, Fibrotic versus homeostatic. P-value calculated by two-sided t-test. g-i, Stereo-seq data from an old murine liver. g, Schematic depiction of the production and processing steps used to generate the Stereo-seq data. h, Visualization of the cell type-enriched hotspots after trimming with Gaussian filtering. i, Abundance of Trm_Pdcd1high projected onto the spatial UMAP of the old liver. EC, endothelial cell. FB, Fibroblast.
