Fig 1.
Pathological examination of the mouse lung tissues.
The mouse lung tissues were fixed, sectioned at 4 μm thickness, and stained with H&E solution, magnification ×200. The alveolar dilatation was obvious, and some of the alveolar septal rupture showed blistering emphysema. There was a small amount of inflammatory cell infiltration near the small bronchial branches (terminal bronchioles, etc.), mainly lymphocytoplasmic cell infiltration.
Fig 2.
scATAC-seq data analysis of the mouse lung tissues.
a: The two approaches used for this project are scATAC-seq (top) and scRNA-seq (bottom). b: UMAP plot showing the integrated cell profiles of scATAC-seq from both case and control mouse lung. The dots indicate individual cells, and the cell-type identity is indicated by color. c: Distribution comparison of mouse genome features and calling peaks annotations. Genome features including Promoter, 5′ UTR, 3′ UTR, Exon, Intron, Downstream and the Distallntergenic; d: Distribution of peaks annotation on the mouse genome of each cell type. Genome features including Promoter, 5’UTR, 3’UTR, Exon, Intron, Downstream, and Distallntergenic. Colors represent different cell types. e: The track visualization of genome-wide cis-regulatory interaction networks for certain regions across specific genes for specific cell types between case and control groups. The gene and cell type are indicated on the head of each figure. The bin size of each window was located in the top left corner. The are color represents different peak accessibility degrees. f: The motif footprints signal of specific TF within 4 kb windows. Red represents the case group, while blue represents the control group. g: The Bubble Chart showing KEGG enrichments for markers of each cell type in the case (upper) and control (down) groups. The color represents the P-value, and cell types are indicated on the x-axis.
Fig 3.
scRNA-seq data analysis of the mouse lung tissues.
a: UMAP plot showing scRNA-seq profiles of cells in the lung. The dots indicate individual cells, and the cell-type identity is indicated by color; b: Bar plot showing the cell type composition in each sample of the scRNA-seq (top). UMAP plot showing scRNA-seq profiles of cells. The dots indicate individual cells, and the group identity is indicated by color (bottom); c: Distribution of percentage of cell in each cell type for DEG between case and control; d: The heatmap showing GO enrichments for each cell type DEG between case and control; e: The heatmap showing TF in case and control; f: Distribution of percentage of Cell interaction in each cell type.
Fig 4.
Integration of scATAC-seq and scRNA-seq data in the mouse lung tissues. a: Integration UMAP plot of scRNA-seq and scATAC-seq data.
Colors indicate each dataset; b: Integration UMAP plot of scRNA-seq and scATAC-seq data. Colors represent different cell types. c: Heatmap showing the gene scores (left) and gene expression (right) of cell type-specific expression genes across 200 pseudobulk samples (Methods). Rows were clustered using k-means clustering (k = 20). For visualization, 10,000 rows were randomly sampled (top). Cell profile of each sample for both scRNA-seq and scATAC-seq data (Middle). The proportion of cells in each sample that were broadly classified cell type (bottom); d: Cell types of TNF signaling pathway-enriched and schematic diagram of the TNF Signaling pathway; e: Specific gene expression profile of scRNA-seq data and corresponding tracks displaying the aggregate accessibility of scATAC-seq data in case and control group.