DOI: 10.6084/m9.figshare.26555948
title: Additional file 1 of Single-cell transcriptomic analysis reveals differential cell subpopulations and distinct phenotype transition in normal and dissected ascending aorta

description: Additional file 1. Supplementary Figure I. Eight cell types in aortic tissues from control and ATAD group revealed by scRNA-seq. A, intraoperative identified ATAD and resected ascending aortic tissues. B, After washing by sterile PBS to remove residual blood and thrombus, ATAD samples were stored in preserving buffer for scRNA-seq. C, t-SNE plot exhibited all 14 clusters and 8 cell types identified in this study. D, the proportion of each cell type in control and ATAD group. The dashed line showed the boundary to discriminate the dominance of each cell type in control or ATAD group. E, the heatmap of marker genes for each cluster. F, t-SNE plots to show the expressions of representative marker genes for each cell type. Supplementary Figure II. The composition of VSMCs subpopulations in each sample and characteristics for each cluster of VSMCs. A, integrative t-SNE plot displayed the composition of VSMCs subpopulations for each sample. VSMCs was not identified from ATAD 5. B-C, t-SNE and violin plots showed the expressions of other representative marker genes. D, heatmap to identify functional modules of genes distinctly expressed in subpopulations of VSMCs. E-J, GO analysis for genes distinctly expressed in subpopulations of VSMCs that was not shown in Fig.2. Supplementary Figure III. The composition of FBs subpopulations in each sample and features for each cluster of FBs. A, integrative t-SNE plot showed the composition of each subpopulation of FBs in each sample. B-C, t-SNE and violin plots revealed the expression of other representative marker genes for subpopulations of FBs. D, heatmap to identify functional modules of genes distinctly expressed in subpopulations of FBs. E-F, GO analysis for genes distinctly expressed in subpopulations of FBs that was not shown in Fig.3. Supplementary Figure IV. The composition of ECs subpopulations in each sample and characteristics for each cluster of ECs. A, integrative t-SNE plot showed the composition of each subpopulation of ECs in each sample. B, t-SNE and violin plots revealed the expression of other representative marker genes for subpopulations of ECs. C, heatmap to identify functional modules of genes distinctly expressed in subpopulations of ECs. D-I, GO analysis for genes distinctly expressed in subpopulations of ECs that was not shown in Fig.4. Supplementary Figure V. The composition of neutrophils subpopulations in each sample and characteristics for each cluster of neutrophils. A, integrative t-SNE plot showed the composition of each subpopulation of neutrophils in all samples. B, t-SNE and violin plots revealed the expressions of other representative marker genes for subpopulations of neutrophils. C, heatmap to identify functional modules of genes distinctly expressed in subpopulations of neutrophils. D-I, GO analysis for genes distinctly expressed in subpopulations of neutrophils that was not shown in Fig.5. Supplementary Figure VI. The composition of monocytes subpopulations in each sample and characteristics for each cluster of monocytes. A, integrative t-SNE plot showed the composition of each subpopulation of monocytes in all samples. B, t-SNE and violin plots revealed the expressions of other representative marker genes for subpopulations of monocytes. C, heatmap to identify functional modules of genes distinctly expressed in subpopulations of monocytes. D-J, GO analysis for genes distinctly expressed in subpopulations of monocytes. Supplementary Figure VII. The composition of macrophages subpopulations in each sample and characteristics for each cluster of macrophages. A, integrative t-SNE plot showed the composition of each subpopulation of macrophages in all samples. B, t-SNE and violin plots revealed the expressions of other representative marker genes for subpopulations of macrophages. C, heatmap to identify functional modules of genes distinctly expressed in subpopulations of macrophages. D-H, GO analysis for genes distinctly expressed in subpopulations of macrophages. Supplementary Figure VIII. Identification of T cell and NK cell as well as their expressions of marker genes. Supplementary Figure IX. The composition of T cells in control and ATAD group as well as cell differentiation trajectory and gene expression alteration of FBs among the differentiation trajectory. A, t-SNE plot showed 5 subpopulations of T cells upon re-clustering. B, the proportion of each subpopulation in T cells. The dashed line discriminated the dominance of each subpopulation in control and ATAD group. C, heatmap of marker genes for each subpopulation of T cells. D, t-SNE and violin plots showed the expressions of representative marker genes for each subpopulation of T cells. E, the separated differentiation trajectory of FBs. F, the distribution of each subpopulation for FBs among the differentiation trajectory. G, alteration curves of other genes that was not shown in Fig.7. The full line represented cell fate 1, the dashed line represented cell fate 2. H-I, heatmap and curves of gene expression alteration relating to mRNA and translational processes. The full line represented cell fate 1, the dashed line represented cell fate 2. J-K, heatmap and curves of gene expression alteration relating to cell death and protein modification. The full line represented cell fate 1, the dashed line represented cell fate 2. Supplementary Figure X. These bubble plots showed the interactions between VSMCs and subpopulations of FBs when FBs were selected as the origins of receptors. Supplementary Figure XI. These bubble plots showed the interactions between VSMCs and subpopulations of neutrophils when they were selected as the origins of receptors. Supplementary Figure XII. The cell differentiation trajectory and gene expression alteration of VSMCs and neutrophils. A , the separated cell differentiation trajectory for each subpopulation of VSMCs. B, the distribution for each subpopulation of VSMCs among the differentiation trajectory. C, heatmap of gene expression alteration relating to glycolysis in subpopulations of VSMCs. D, alteration curves of other genes in subpopulations of VSMCs. The full line represented cell fate 1, the dashed line represented cell fate 2. E-G, GO analysis for 3 clusters of altered genes in subpopulations of FBs. H, the separated cell differentiation trajectory for each subpopulation of neutrophils. I, the distribution for each subpopulation of neutrophils among the differentiation trajectory. J, heatmap of gene expression alteration relating to immune response and Th1 cell activation in subpopulations of neutrophils. K, alteration curves of other genes in subpopulations of neutrophils. The full line represented cell fate 1, the dashed line represented cell fate 2. L-N, GO analysis for 3 clusters of altered genes in subpopulations of neutrophils. Supplementary Figure XIII. The networks and functions for gene modules identified by WGCNA among neutrophils, VSMCs and FBs. A-H, the networks and functions for gene modules identified by WGCNA that were not shown in Fig.8. Supplementary Figure XIV. Overall expression of dissociation-induced IEGs in each subpopulation. A, correlation analysis among all subpopulations on the basis of top 2000 variable genes. B, overall expression of dissociation-induced IEGs in each subpopulation. The red label represented positive expression of dissociation-induced IEGs. The green label represented positive expression of dissociation-induced IEGs. Supplementary Figure XV. Expressions of C1QA and C1QB in non-immune cells including VSMCs, FBs and ECs. Supplementary file I. Separated cell cluster and marker gene of each cell type for all samples in this study. Supplementary file II. Patient demographics that were performed scRNA-seq. Supplementary file III. Genes that were used to identify functions of VSMCs and FBs markers of neutrophils. Supplementary file IV. The regulatory intensity results of CXCL12-ACKR3 between VSMCs 1 and FBs based on CellPhone database. Supplementary file V. The gene list of dissociation-induced IEGs. Supplementary file VI. The list of antibodies used in IHC and IF.