Extended Data Fig. 6: FiNi-seq enriches fibroblast clusters that bear distinct characteristics.
FiNi-seq and control cells were obtained from young and old livers and sequenced with FiNi-seq and conventional scRNA-seq, respectively. a, Number of fibroblasts in the indicated organs (left) and subtypes within the liver (right), as determined by the pan-organ fibroblast atlas. b, Dot plot showing clusters that expressed hepatic stellate cell (HSC) and fibroblast markers. c, Bar plot showing the proportions of HSCs and the fibroblast subtypes in the four samples. Number of biological replicates: YC (n = 3), YF (n = 3), OC (n = 6), OF (n = 5). The data are presented as mean ± s.e. P-value is determined with two-sided Wilcoxon rank-sum test. HSC: YC vs OF, p = 0.0357; YC vs OC, p = 0.0219; YF vs OF, p = 0.0357; YF vs OC, p = 0.0219; FB_Wif1: YC vs OF, p = 0.0357; YF vs OC, p = 0.0162; OC vs OF, p = 0.0055; FB_Smoc1: YF vs OF, p = 0.0357; OC vs OF, p = 0.0067; FB_Portal: YC vs OC, p = 0.0431; YF vs OC, p = 0.0219; OC vs OF, p = 0.0116. d, Number of the total and mesenchymal cells that were captured in the Tabula Muris Senis study18 and in our present study. Young and old control tissue counts were combined, as were young and old FiNi-seq counts. e, UMAP projection of major cell-type clusters in the dataset of young, old and CCl4. f, Top, UMAP projection of CCl4 included dataset by condition. Bottom, Barplot showing proportion of mesenchymal cell, comparing control and FiNi-seq by conditions. g, UMAP projection of mesenchymal cells subtypes in CCl4 included dataset. (fix label after confirm) h, IF staining of FB_Wif1 marker (WIF1) and fibroblast lineage marker (PDGFRA) in young and old liver (left) with bar plot comparison of WIF1 + PDGFRA+ cells in young and old liver (right) (two-sided t-test, p = 0.0038). Each group comprised three biological replicates. The data are presented as mean ± s.e. i, RNAscope assay with staining of the FB_Wif1 (top) and FB_Smoc1 (bottom) fibroblasts in the young (left) and old (right) liver without DAPI. The fibroblast-lineage marker Pdgfra were combined with FB_Wif1 marker Phex, and FB_Smoc1 marker Fmod. j, RNAscope assay showing the FB_Wif1, FB_Smoc1, and Fibrotic EC in old female liver. FB, fibroblast.
