Fig. 6: Combining MERFISH and snRNA-seq to analyze fibrotic livers.
From: Spatial transcriptomics of healthy and fibrotic human liver at single-cell resolution
a UMAP of snRNA-seq data for injured human liver. Annotations for the hepatocytes were determined by merging data from both MERFISH and snRNA-seq and leveraging both marker gene expression and label-transfer of MERFISH labels. b Heatmap displaying differentially expressed genes that identify each snRNA-seq cluster. Normalized expression level is indicated by the color bar on the right. Each column represents a single nucleus, and nuclei are grouped by cluster as indicated at the top of the heatmap. Genes are indicated at the bottom of the heatmap, groups of genes characteristics of individual cell clusters are indicated on the top, and cells are grouped by cluster as indicated by color at the left. c Dot plot quantifying expression of genes differentially expressed in clusters seen in healthy measurements (Healthy zone 1, 2, or 3) or in fibrotic samples (Portal Hep, Central Hep, Fibrotic Hep 1, or Fibrotic Hep 2) for hepatocytes. Dot plots quantifying expression of genes differentially expressed in macrophages (d) and HSCs (e) are shown. Macs Healthy 1 and Healthy 2 refer to Mac 1 and Mac 2 cells in healthy liver, and HSCs Healthy 1 and Healthy 2 refer to HSC 1 and HSC 2 cells in healthy liver.
