A single-cell transcriptome atlas of pig skin characterizes anatomical positional heterogeneity
- Department of Zoology, College of Life Science, Sichuan Agricultural University, China
- Chengdu Livestock and Poultry Genetic Resources Protection Center, China
- BGI Beijing Genome Institute, China
- College of Animal Science and Technology, Sichuan Agricultural University, China
Figures
Figure 1 with 3 supplements
Single-cell transcriptome profiling of different skin anatomical sites in CH pig.
(A) Flowchart overview of skin single-cell RNA sequencing from different anatomical skin regions of CH pigs. (B) The t-SNE plot visualization showing 21 clusters of annotated cell types from CH pig …
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Figure 1—source data 1
Source data of marker genes for each cluster in Figure 1C.
- https://cdn.elifesciences.org/articles/86504/elife-86504-fig1-data1-v1.xlsx
Figure 1—figure supplement 1
The count of genes/unique molecular identifier (UMI) and the expression of marker genes.
(A) Violin plot showing the number of genes detected from different skin sites. (B) Violin plot showing the UMI count detected from different skin sites. (C) Violin plot showing the genes expression …
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Figure 1—figure supplement 1—source data 1
Source data of the gene/unique molecular identifier (UMI) counts in Figure 1—figure supplement 1A and B.
- https://cdn.elifesciences.org/articles/86504/elife-86504-fig1-figsupp1-data1-v1.xlsx
Figure 1—figure supplement 2
The cell types of different skin regions.
(A) UMAP visualization of cell types from different skin regions in global Chenghua (CH) skin cells. The number of cell types in different skin regions. (B) The cell types of individual skin sites …
Figure 1—figure supplement 3
Comparison of skin cells among human, pig, and mouse species.
(A) The t-SNE plot visualization of all cell types for skin cells among human, pig, and mouse. (B) Violin plots showing the number of unique molecular identifier (UMI) and gene counts of skin cells …
Figure 2
Heterogeneity of skin smooth muscle cells (SMCs) in different anatomical sites.
(A) The t-SNE plot visualization of SMCs including clusters 0, 2, 5, 6, and 13. (B) Confocal images showing immunofluorescence staining of ACTA2 (green) and MYH11 (red) in back skin sections, …
Figure 3
Heterogeneity of skin smooth muscle cells (SMCs) in different anatomical sites.
(A) The cell number of SMC subpopulations in different skin regions. (B) Heatmap showing the differentially expressed genes of SMCs in multiple compared groups. Red represents upregulated genes, …
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Figure 3—source data 1
Source data of the differentially expressed genes of smooth muscle cells (SMCs) in multiple compared groups in Figure 3B.
- https://cdn.elifesciences.org/articles/86504/elife-86504-fig3-data1-v1.xlsx
Figure 4 with 2 supplements
Heterogeneity of skin endothelial cells (ECs) in different anatomical sites.
(A) The t-SNE plot visualization of ECs. (B) Immunofluorescence staining of APOA1 (green) and PECAM1 (red) in back skin sections, representative markers of ECs. Scale bar = 50 μm. n = 3. (C) Dot …
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Figure 4—source data 1
Source data of the differentially expressed genes of endothelial cells (ECs) in multiple compared groups in Figure 4G.
- https://cdn.elifesciences.org/articles/86504/elife-86504-fig4-data1-v1.xlsx
Figure 4—figure supplement 1
Heterogeneity of skin endothelial cells (ECs) in different anatomical sites.
(A) The enriched Gene Ontology (GO) terms pertaining to biological process for each ECs subpopulation were sorted by q-value. (B) Heatmap of gene expression for focal adhesion pathway among ECs …
Figure 4—figure supplement 2
Heterogeneity of skin endothelial cells (ECs) in different anatomical sites.
Heatmap of gene expression in focal adhesion pathway (A), cell adhesion molecule (B) pathway, and other immune pathways (C) among ECs subpopulations of different skin regions.
Figure 5 with 2 supplements
Heterogeneity of skin fibroblasts (FBs) in different anatomical sites.
(A) Skin section with HE staining (left) and dermal thickness of six different sites (right) including head, ear, back, shoulder, abdomen, and leg. Scale bar = 100 μm. n = 3. (B) The t-SNE plot …
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Figure 5—source data 1
Source data of the differentially expressed genes of fibroblasts (FBs) in multiple compared groups in Figure 5E.
- https://cdn.elifesciences.org/articles/86504/elife-86504-fig5-data1-v1.xlsx
Figure 5—figure supplement 1
Heterogeneity of skin fibroblasts (FBs) in different anatomical sites.
(A) The skin specimens and thickness of different sites. Left is skin thickness, and right is skin specimens. (B) Skin sections of different regions. Scar bar = 1000 μm. n = 3. (C) The enriched Gene …
Figure 5—figure supplement 2
Heterogeneity of skin fibroblasts (FBs) in different anatomical sites.
(A) Unsupervised hierarchical clustering showing the transcriptional profile of 417 differentially expressed genes (DEGs) in clusters 1, 8, 9, and 12 of FBs. (B) Regulatory network of DEGs of FBs of …
Figure 6 with 1 supplement
Heterogeneity of skin cells in different pig populations.
(A) Skin section with HE staining (left) and dermal thickness of back skin between Chenghua (CH) and large white (LW) pig (right). Scale bar = 100 μm. n = 3. (B) The t-SNE plot visualization of all …
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Figure 6—source data 1
Source data of marker genes for each cluster in Figure 6C.
- https://cdn.elifesciences.org/articles/86504/elife-86504-fig6-data1-v1.xlsx
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Figure 6—source data 2
Source data of the differentially expressed genes of smooth muscle cells (SMCs), endothelial cells (ECs), and fibroblasts (FBs) in the compared group in Figure 6E.
- https://cdn.elifesciences.org/articles/86504/elife-86504-fig6-data2-v1.xlsx
Figure 6—figure supplement 1
Heterogeneity of skin cells in different pig populations.
(A) Skin specimens and sections of Chenghua (CH) and large white (LW) pig. Left is skin specimens, and right is skin sections. Scar bar = 1000 μm. n = 3. (B) Violin plot showing the number of genes …
Figure 7 with 1 supplement
Signaling crosstalk among various cell types in skin.
(A) Circle plot representing the cell communication among cell types. Circle sizes represent the number of cells, and edge width represents the communication probability. Hierarchical plot showing …
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Figure 7—source data 1
Cell communication of skin cells in Figure 7A.
- https://cdn.elifesciences.org/articles/86504/elife-86504-fig7-data1-v1.xlsx
Figure 7—figure supplement 1
Signaling crosstalk among various cell types in skin.
(A) Circle plot representing the cell communication among cell types in the COLLAGEN/LAMININ signaling pathways. Edge width represents communication probability. (B) Relative contribution of each …
