Fig. 2: snRNA-seq2 allows deep profiling of single nuclei including key liver-specific transcription factors and downstream target genes involved in healthy homeostasis and chronic liver disease.
From: Single-nucleus RNA-seq2 reveals functional crosstalk between liver zonation and ploidy
A Heatmap showing the gene expression of the top five differentially expressed genes in forty randomly selected nuclei per cell type (colored by log-transformed, normalized counts). Ploidy analysis shows that 4n nuclei are enriched in the hepatocyte cluster. B Cell cycle analysis using Cyclone shows that the majority of nuclei are in G1 phase. tSNEs colored by ploidy (top), assigned cell cycle phase (middle), and G1 score (bottom). Table showing the number of nuclei that are in each assigned phase for diploid and tetraploid nuclei from the hepatocyte cluster. C tSNE colored by the expression of key liver-specific transcription factors involved in liver homeostasis and hepatic function. D Dot plot shows that the expression levels (color scale) and the percentage (dot size) of cells expressing key transcription factors can be dissected between 2n and 4n nuclei. E tSNEs colored by the expression of disease-related marker genes, separated into two main categories of liver disease: non-alcoholic fatty liver disease/non-alcoholic steatohepatitis (NAFLD/NASH) and fibrosis/hepatocellular carcinoma (HCC), showing cellular heterogeneity in different cell populations. F Dot plot showing the expression of the disease-related marker genes across cell types in young wild-type mice livers.
