Extended Data Fig. 3: Characterization of scRNA-seq data.
From: A spatiotemporal atlas of cholestatic injury and repair in mice
a. Expression of top DEGs (log2foldchange ≥ 0.25, q < 0.05) for each annotated cell type in scRNA-seq. b. GSEA analysis of reported RRG (reprogramming-related genes) in LPLC and hepatocyte pseudo-bulk scRNA-seq data during DDC injury. c. Adgre1, Clec4f, and LAM marker (Gpnmb and Fabp5) on non-KC macrophage UMAP of scRNA-seq. d. GSEA analysis of reported LAM-enriched genes in non-KC macrophages and KC pseudo-bulk scRNA-seq data during DDC injury. e. UMAP of dynamics of indicated cell types in scRNA-seq data at D0 and D17. Circle stood for the LAM populations. f. Magnified view of the cholangiocyte in the area selected from Fig. 1h and immunofluorescence staining for Ck19 (yellow) in the matched area from an adjacent section. Scale bar, 100 μm. g. Spatial correspondence of spatial ___domain and RCTD deconvolution result on a representative D17 slide. Left panel indicated the comparison of chol-___domain and cholangiocyte in RCTD. Right panel indicated the comparison of LPLC-___domain and LPLC in RCTD. Green points stood for the overlap bins of two methods. Scale bar, 500 μm.
