Additional file 1 of Single-cell transcriptome analysis reveals liver injury induced by glyphosate in mice
Creators: name: Wu, Jiangpeng
name: Sun, Xiuping
name: Wu, Chunyi
name: Hong, Xiaoping
name: Xie, Lulin
name: Shi, Zixu
name: Zhao, Liang
name: Du, Qingfeng
name: Xiao, Wei
name: Sun, Jichao
name: Wang, Jigang
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Fig. S1. Quality control for scRNA-seq. (A) Criteria for the degree of necrosis (left). Histopathological evaluation for all samples (right). (B) Consistency (nFeature_RNA, nCount_RNA, percent.mt) of cell capture and identification for each sample (left) and the two groups (right) after scRNA-seq data quality control. nFeature_RNA, nCount_RNA and percent.mt represent the number of genes, the number of transcripts and the percentage of mitochondrial genes of each cell, respectively. Fig. S2. Single-cell analysis of 13 major cell lineages. (A) UMAP showing all clusters from the control and GLY-treated groups. (B) Merged UMAP plot for all samples. (C) Heatmap of top 100 DEGs for major cell types. (D) Distribution comparison of the major cell clusters between the control and GLY-treated groups. (E) Histograms depicting the proportional changes of each cell type for individual samples (left) and the combined control and GLY-treated samples (right). Fig. S3. Single-cell analysis of HSCs. (A) UMAP showing all subclusters of HSCs from the control and GLY-treated groups. (B) Merged UMAP plot for all samples. (C) Proportional changes of each cell subtype for the two groups. (D) Pseudotime trajectory analysis implying the development of HSC subtypes. (E) Histogram displaying the proportional changes of the two groups under different states during the pseudotime analysis. (F) Violin plots showing the cell-cycle-related genes of each HSC subtypes. Fig. S4. Single-cell analysis of hepatocytes. (A) UMAP showing hepatocytes composed of three subclusters from the control and GLY-treated groups. (B) Merged UMAP plot for hepatocytes of all samples. (C) UMAP depicting the distribution of hepatocyte subclusters from the control and GLY-treated groups. (D) Histogram displaying the proportional changes of each subtype for every sample. (E) Boxplot of ROS score for the two groups. P value is from wilcox.test (unpaired and two-tailed); *P &lt; 0.05. Fig. S5. Single-cell analysis of KCs. (A) UMAP showing all subclusters of KCs from the control and GLY-treated groups. (B) Dotplot showing the expression of representative markers in each KC subcluster. (C) Merged UMAP plot for all samples. (D) Histogram demonstrating the proportional changes of each KC subcluster for each sample. (E) UMAP displaying the distribution of each KC subcluster from the control and GLY-treated groups. (F) Boxplot of phagocytosis score for the two groups. P value is from wilcox.test (unpaired and two-tailed); ***P &lt; 0.001, **P &lt; 0.01, *P &lt; 0.05. (G) Boxplot of ROS score for the two groups. P value is from wilcox.test (unpaired and two-tailed); ***P &lt; 0.001. (H) Violin plots showing the expression levels of Cd68 genes for two groups in all cell clusters. Fig. S6. Single-cell analysis of LCMs. (A) UMAP showing the cell subclusters of LCMs from the control and GLY-treated groups. (B) Merged UMAP plot for all the samples. (C) Histogram visualizing the proportional changes of each LCM subtype for each sample. (D) Heatmap of all DEGs for the three LCM subtypes (left) and their corresponding functional enrichment analysis (right). (E) Venn diagram for the downregulated genes of each LCM subcluster after GLY treatment. (F) UMAP showing the expression level of Spp1 in LCM subtypes of the two groups. (G) Boxplot of inflammatory response score for the two groups. (H) Boxplot of ROS score for the two groups. P value is from wilcox.test (unpaired and two-tailed); **P &lt; 0.01. (I) Heatmap displaying the differentially expressed cytokines in each LCM subtype after GLY treatment. Fig. S7. Cell–cell communication analysis for major cell clusters. (A) The overall networks of cell–cell communication within different cell types for control and GLY groups. (B) The interaction strength of each cell type for control and GLY groups. (C) The change for SPP1 signaling pathway network after GLY treatment. (D) Detailed ligand–receptor interactions of the SPP1 signaling pathway for LCM cells. (E) Signaling pathways presented only in the GLY group. (F) Upregulated and downregulated signaling after GLY treatment. Fig. S8. Cell–cell communication analysis. (A) Histogram showing the numbers of inferred interactions and interaction strength of the control and GLY-treated groups. (B) Chord diagram exhibiting the numbers of inferred interactions of LCMs and KCs for the two groups. (C) Histogram displaying the relative information flow of the two groups. (D) Dotplot depicting the ligand–receptor pairs between LCMs and major cell lineages. (E) Chord diagram demonstrating the signaling pathways present only in the control group. (F) Violin plots showing the expression levels of ligand–receptor genes of the Spp1 signaling pathway for major cell lineages.