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LitCovid-PubTator

LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T57","span":{"begin":1329,"end":1335},"obj":"Body_part"},{"id":"T58","span":{"begin":1499,"end":1505},"obj":"Body_part"},{"id":"T59","span":{"begin":1583,"end":1589},"obj":"Body_part"},{"id":"T60","span":{"begin":2007,"end":2013},"obj":"Body_part"},{"id":"T61","span":{"begin":2037,"end":2043},"obj":"Body_part"}],"attributes":[{"id":"A57","pred":"uberon_id","subj":"T57","obj":"http://purl.obolibrary.org/obo/UBERON_0001723"},{"id":"A58","pred":"uberon_id","subj":"T58","obj":"http://purl.obolibrary.org/obo/UBERON_0001723"},{"id":"A59","pred":"uberon_id","subj":"T59","obj":"http://purl.obolibrary.org/obo/UBERON_0001723"},{"id":"A60","pred":"uberon_id","subj":"T60","obj":"http://purl.obolibrary.org/obo/UBERON_0000344"},{"id":"A61","pred":"uberon_id","subj":"T61","obj":"http://purl.obolibrary.org/obo/UBERON_0001723"}],"text":"Single cell RNA-seq analysis of oral tissues\nSingle cell RNA-seq was utilized for four oral tissues, and the data was analyzed to confirm the above results and assess the cell type-specific expression of ACE2. After the data preprocessing (shown in section “Materials and methods”), 22 969 cells were acquired and 7 cell types were identified (Fig. 2a), including epithelial cells (marker genes including SFN, KRT6A, and KRT10), fibroblasts (marker genes including FAP, PDPN, COL1A2, DCN, COL3A1, COL6A1), T cells (marker genes including CD2, CD3D, CD3E, and CD3G), macrophages (marker genes including CD163, CSF1R, CD68, and FCGR2A), mast cells (marker genes including CMA1, MS4A2, TPSAB1, TPSB2), B cells (marker genes including SLAMF7, FCRL5, and CD79A) and endothelial cells (marker genes including PECAM1, VWF, and ENG). The heatmap of main cell markers across the cell types can be found in Fig. 2b.\nFig. 2 Single cell RNA-seq analysis of oral tissues from independent dataset. a Seven-cell types were identified by the cell markers; cells were clustered by UMAP method. b Heatmap of cell markers for identifying cell types. c Scatter plots of all the cells with ACE2 expression. d Violin plot of ACE2 expression across different oral sites. e Violin plot of ACE2 expression across different cell types. f Scatter plots of tongue epithelial cells with ACE2 expression\nAccording to Fig. 2c, d, we confirmed the ACE2 was expressed in oral tissues (0.52% ACE2-positive cells), and higher in oral tongue than buccal and gingival tissues (95.86% ACE2-positive cells located in oral tongue). Figure 2e shows that the ACE2-positive cells could be found in oral tissues including epithelial cells (1.19% ACE2-positive cells), T cells (\u003c0.5%), B cells (\u003c0.5%), and fibroblast (\u003c0.5%), and the ACE2 was highly enriched in epithelial cells, of which 93.38% ACE2-positive cells belong to epithelial cells (Fig. 2f). The above results indicated that the ACE2 could be expressed on the epithelial cells of the oral mucosa and highly enriched in tongue epithelial cells."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T28","span":{"begin":465,"end":468},"obj":"Disease"},{"id":"T29","span":{"begin":543,"end":547},"obj":"Disease"}],"attributes":[{"id":"A28","pred":"mondo_id","subj":"T28","obj":"http://purl.obolibrary.org/obo/MONDO_0021055"},{"id":"A29","pred":"mondo_id","subj":"T29","obj":"http://purl.obolibrary.org/obo/MONDO_0014280"}],"text":"Single cell RNA-seq analysis of oral tissues\nSingle cell RNA-seq was utilized for four oral tissues, and the data was analyzed to confirm the above results and assess the cell type-specific expression of ACE2. After the data preprocessing (shown in section “Materials and methods”), 22 969 cells were acquired and 7 cell types were identified (Fig. 2a), including epithelial cells (marker genes including SFN, KRT6A, and KRT10), fibroblasts (marker genes including FAP, PDPN, COL1A2, DCN, COL3A1, COL6A1), T cells (marker genes including CD2, CD3D, CD3E, and CD3G), macrophages (marker genes including CD163, CSF1R, CD68, and FCGR2A), mast cells (marker genes including CMA1, MS4A2, TPSAB1, TPSB2), B cells (marker genes including SLAMF7, FCRL5, and CD79A) and endothelial cells (marker genes including PECAM1, VWF, and ENG). The heatmap of main cell markers across the cell types can be found in Fig. 2b.\nFig. 2 Single cell RNA-seq analysis of oral tissues from independent dataset. a Seven-cell types were identified by the cell markers; cells were clustered by UMAP method. b Heatmap of cell markers for identifying cell types. c Scatter plots of all the cells with ACE2 expression. d Violin plot of ACE2 expression across different oral sites. e Violin plot of ACE2 expression across different cell types. f Scatter plots of tongue epithelial cells with ACE2 expression\nAccording to Fig. 2c, d, we confirmed the ACE2 was expressed in oral tissues (0.52% ACE2-positive cells), and higher in oral tongue than buccal and gingival tissues (95.86% ACE2-positive cells located in oral tongue). Figure 2e shows that the ACE2-positive cells could be found in oral tissues including epithelial cells (1.19% ACE2-positive cells), T cells (\u003c0.5%), B cells (\u003c0.5%), and fibroblast (\u003c0.5%), and the ACE2 was highly enriched in epithelial cells, of which 93.38% ACE2-positive cells belong to epithelial cells (Fig. 2f). The above results indicated that the ACE2 could be expressed on the epithelial cells of the oral mucosa and highly enriched in tongue epithelial cells."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T13","span":{"begin":465,"end":468},"obj":"Chemical"}],"attributes":[{"id":"A13","pred":"chebi_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/CHEBI_73617"}],"text":"Single cell RNA-seq analysis of oral tissues\nSingle cell RNA-seq was utilized for four oral tissues, and the data was analyzed to confirm the above results and assess the cell type-specific expression of ACE2. After the data preprocessing (shown in section “Materials and methods”), 22 969 cells were acquired and 7 cell types were identified (Fig. 2a), including epithelial cells (marker genes including SFN, KRT6A, and KRT10), fibroblasts (marker genes including FAP, PDPN, COL1A2, DCN, COL3A1, COL6A1), T cells (marker genes including CD2, CD3D, CD3E, and CD3G), macrophages (marker genes including CD163, CSF1R, CD68, and FCGR2A), mast cells (marker genes including CMA1, MS4A2, TPSAB1, TPSB2), B cells (marker genes including SLAMF7, FCRL5, and CD79A) and endothelial cells (marker genes including PECAM1, VWF, and ENG). The heatmap of main cell markers across the cell types can be found in Fig. 2b.\nFig. 2 Single cell RNA-seq analysis of oral tissues from independent dataset. a Seven-cell types were identified by the cell markers; cells were clustered by UMAP method. b Heatmap of cell markers for identifying cell types. c Scatter plots of all the cells with ACE2 expression. d Violin plot of ACE2 expression across different oral sites. e Violin plot of ACE2 expression across different cell types. f Scatter plots of tongue epithelial cells with ACE2 expression\nAccording to Fig. 2c, d, we confirmed the ACE2 was expressed in oral tissues (0.52% ACE2-positive cells), and higher in oral tongue than buccal and gingival tissues (95.86% ACE2-positive cells located in oral tongue). Figure 2e shows that the ACE2-positive cells could be found in oral tissues including epithelial cells (1.19% ACE2-positive cells), T cells (\u003c0.5%), B cells (\u003c0.5%), and fibroblast (\u003c0.5%), and the ACE2 was highly enriched in epithelial cells, of which 93.38% ACE2-positive cells belong to epithelial cells (Fig. 2f). The above results indicated that the ACE2 could be expressed on the epithelial cells of the oral mucosa and highly enriched in tongue epithelial cells."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T53","span":{"begin":0,"end":44},"obj":"Sentence"},{"id":"T54","span":{"begin":45,"end":209},"obj":"Sentence"},{"id":"T55","span":{"begin":210,"end":825},"obj":"Sentence"},{"id":"T56","span":{"begin":826,"end":905},"obj":"Sentence"},{"id":"T57","span":{"begin":906,"end":1373},"obj":"Sentence"},{"id":"T58","span":{"begin":1374,"end":1591},"obj":"Sentence"},{"id":"T59","span":{"begin":1592,"end":1909},"obj":"Sentence"},{"id":"T60","span":{"begin":1910,"end":2061},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Single cell RNA-seq analysis of oral tissues\nSingle cell RNA-seq was utilized for four oral tissues, and the data was analyzed to confirm the above results and assess the cell type-specific expression of ACE2. After the data preprocessing (shown in section “Materials and methods”), 22 969 cells were acquired and 7 cell types were identified (Fig. 2a), including epithelial cells (marker genes including SFN, KRT6A, and KRT10), fibroblasts (marker genes including FAP, PDPN, COL1A2, DCN, COL3A1, COL6A1), T cells (marker genes including CD2, CD3D, CD3E, and CD3G), macrophages (marker genes including CD163, CSF1R, CD68, and FCGR2A), mast cells (marker genes including CMA1, MS4A2, TPSAB1, TPSB2), B cells (marker genes including SLAMF7, FCRL5, and CD79A) and endothelial cells (marker genes including PECAM1, VWF, and ENG). The heatmap of main cell markers across the cell types can be found in Fig. 2b.\nFig. 2 Single cell RNA-seq analysis of oral tissues from independent dataset. a Seven-cell types were identified by the cell markers; cells were clustered by UMAP method. b Heatmap of cell markers for identifying cell types. c Scatter plots of all the cells with ACE2 expression. d Violin plot of ACE2 expression across different oral sites. e Violin plot of ACE2 expression across different cell types. f Scatter plots of tongue epithelial cells with ACE2 expression\nAccording to Fig. 2c, d, we confirmed the ACE2 was expressed in oral tissues (0.52% ACE2-positive cells), and higher in oral tongue than buccal and gingival tissues (95.86% ACE2-positive cells located in oral tongue). Figure 2e shows that the ACE2-positive cells could be found in oral tissues including epithelial cells (1.19% ACE2-positive cells), T cells (\u003c0.5%), B cells (\u003c0.5%), and fibroblast (\u003c0.5%), and the ACE2 was highly enriched in epithelial cells, of which 93.38% ACE2-positive cells belong to epithelial cells (Fig. 2f). The above results indicated that the ACE2 could be expressed on the epithelial cells of the oral mucosa and highly enriched in tongue epithelial cells."}