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LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T25","span":{"begin":133,"end":137},"obj":"Body_part"},{"id":"T26","span":{"begin":138,"end":144},"obj":"Body_part"}],"attributes":[{"id":"A25","pred":"uberon_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A26","pred":"uberon_id","subj":"T26","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"}],"text":"Figure 1 Expression of ACE2 in Type II Pneumocytes in Healthy Lungs of Non-human Primates\n(A) Schematic of protocol for isolation of lung tissue at necropsy from healthy non-human primates (M. mulatta, n = 3), creation of scRNA-seq libraries by using Seq-Well v1, and computational analysis to identify cell types by using unbiased methods. UMAP projection of 3,793 single cells, points colored by cell identity (see STAR Methods).\n(B) Uniform manifold approximation and projection (UMAP) as in (A), points colored by detection of ACE2 (coronavirus receptor, top) or TMPRSS2 (coronavirus S protein priming for entry, bottom). Color coding is as follows: black, RNA positive; blue, RNA negative.\n(C) Dot plot of 2 defining genes for each cell type (Table S1) (Bonferroni-adjusted p \u003c 0.001) and ACE2 and TMPRSS2. Dot size represents fraction of cells within that type expressing a given gene, and color intensity represents binned count-based expression amount (log(scaled UMI+1)) among expressing cells. ACE2 is enriched in type II pneumocytes (6.7% expressing, Bonferroni-adjusted p = 8.62E−33), as is TMPRSS2 (29.5% expressing, Bonferroni-adjusted p = 8.73E−153). Of all type II pneumocytes, 3.8% co-express ACE2 and TMPRSS2 (Table S9). Red arrow indicates cell type with largest proportion of ACE2+TMPRSS2+ cells.\n(D) Genes differentially expressed among ACE2+ and ACE2− type II pneumocytes. (SCDE package, FDR-adjusted p \u003c 0.05 for IFNGR2, NT5DC1, ARL6IP1, and TRIM27; full results can be found in Table S1).\nSee also Table S1."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T86","span":{"begin":417,"end":421},"obj":"Disease"}],"attributes":[{"id":"A86","pred":"mondo_id","subj":"T86","obj":"http://purl.obolibrary.org/obo/MONDO_0010408"}],"text":"Figure 1 Expression of ACE2 in Type II Pneumocytes in Healthy Lungs of Non-human Primates\n(A) Schematic of protocol for isolation of lung tissue at necropsy from healthy non-human primates (M. mulatta, n = 3), creation of scRNA-seq libraries by using Seq-Well v1, and computational analysis to identify cell types by using unbiased methods. UMAP projection of 3,793 single cells, points colored by cell identity (see STAR Methods).\n(B) Uniform manifold approximation and projection (UMAP) as in (A), points colored by detection of ACE2 (coronavirus receptor, top) or TMPRSS2 (coronavirus S protein priming for entry, bottom). Color coding is as follows: black, RNA positive; blue, RNA negative.\n(C) Dot plot of 2 defining genes for each cell type (Table S1) (Bonferroni-adjusted p \u003c 0.001) and ACE2 and TMPRSS2. Dot size represents fraction of cells within that type expressing a given gene, and color intensity represents binned count-based expression amount (log(scaled UMI+1)) among expressing cells. ACE2 is enriched in type II pneumocytes (6.7% expressing, Bonferroni-adjusted p = 8.62E−33), as is TMPRSS2 (29.5% expressing, Bonferroni-adjusted p = 8.73E−153). Of all type II pneumocytes, 3.8% co-express ACE2 and TMPRSS2 (Table S9). Red arrow indicates cell type with largest proportion of ACE2+TMPRSS2+ cells.\n(D) Genes differentially expressed among ACE2+ and ACE2− type II pneumocytes. (SCDE package, FDR-adjusted p \u003c 0.05 for IFNGR2, NT5DC1, ARL6IP1, and TRIM27; full results can be found in Table S1).\nSee also Table S1."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T39","span":{"begin":36,"end":38},"obj":"Chemical"},{"id":"T40","span":{"begin":590,"end":597},"obj":"Chemical"},{"id":"T41","span":{"begin":1029,"end":1031},"obj":"Chemical"},{"id":"T42","span":{"begin":1178,"end":1180},"obj":"Chemical"},{"id":"T43","span":{"begin":1379,"end":1381},"obj":"Chemical"}],"attributes":[{"id":"A39","pred":"chebi_id","subj":"T39","obj":"http://purl.obolibrary.org/obo/CHEBI_74067"},{"id":"A40","pred":"chebi_id","subj":"T40","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A41","pred":"chebi_id","subj":"T41","obj":"http://purl.obolibrary.org/obo/CHEBI_74067"},{"id":"A42","pred":"chebi_id","subj":"T42","obj":"http://purl.obolibrary.org/obo/CHEBI_74067"},{"id":"A43","pred":"chebi_id","subj":"T43","obj":"http://purl.obolibrary.org/obo/CHEBI_74067"}],"text":"Figure 1 Expression of ACE2 in Type II Pneumocytes in Healthy Lungs of Non-human Primates\n(A) Schematic of protocol for isolation of lung tissue at necropsy from healthy non-human primates (M. mulatta, n = 3), creation of scRNA-seq libraries by using Seq-Well v1, and computational analysis to identify cell types by using unbiased methods. UMAP projection of 3,793 single cells, points colored by cell identity (see STAR Methods).\n(B) Uniform manifold approximation and projection (UMAP) as in (A), points colored by detection of ACE2 (coronavirus receptor, top) or TMPRSS2 (coronavirus S protein priming for entry, bottom). Color coding is as follows: black, RNA positive; blue, RNA negative.\n(C) Dot plot of 2 defining genes for each cell type (Table S1) (Bonferroni-adjusted p \u003c 0.001) and ACE2 and TMPRSS2. Dot size represents fraction of cells within that type expressing a given gene, and color intensity represents binned count-based expression amount (log(scaled UMI+1)) among expressing cells. ACE2 is enriched in type II pneumocytes (6.7% expressing, Bonferroni-adjusted p = 8.62E−33), as is TMPRSS2 (29.5% expressing, Bonferroni-adjusted p = 8.73E−153). Of all type II pneumocytes, 3.8% co-express ACE2 and TMPRSS2 (Table S9). Red arrow indicates cell type with largest proportion of ACE2+TMPRSS2+ cells.\n(D) Genes differentially expressed among ACE2+ and ACE2− type II pneumocytes. (SCDE package, FDR-adjusted p \u003c 0.05 for IFNGR2, NT5DC1, ARL6IP1, and TRIM27; full results can be found in Table S1).\nSee also Table S1."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T62","span":{"begin":0,"end":89},"obj":"Sentence"},{"id":"T63","span":{"begin":90,"end":340},"obj":"Sentence"},{"id":"T64","span":{"begin":341,"end":431},"obj":"Sentence"},{"id":"T65","span":{"begin":432,"end":625},"obj":"Sentence"},{"id":"T66","span":{"begin":626,"end":694},"obj":"Sentence"},{"id":"T67","span":{"begin":695,"end":811},"obj":"Sentence"},{"id":"T68","span":{"begin":812,"end":1003},"obj":"Sentence"},{"id":"T69","span":{"begin":1004,"end":1165},"obj":"Sentence"},{"id":"T70","span":{"begin":1166,"end":1238},"obj":"Sentence"},{"id":"T71","span":{"begin":1239,"end":1316},"obj":"Sentence"},{"id":"T72","span":{"begin":1317,"end":1512},"obj":"Sentence"},{"id":"T73","span":{"begin":1513,"end":1531},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Figure 1 Expression of ACE2 in Type II Pneumocytes in Healthy Lungs of Non-human Primates\n(A) Schematic of protocol for isolation of lung tissue at necropsy from healthy non-human primates (M. mulatta, n = 3), creation of scRNA-seq libraries by using Seq-Well v1, and computational analysis to identify cell types by using unbiased methods. UMAP projection of 3,793 single cells, points colored by cell identity (see STAR Methods).\n(B) Uniform manifold approximation and projection (UMAP) as in (A), points colored by detection of ACE2 (coronavirus receptor, top) or TMPRSS2 (coronavirus S protein priming for entry, bottom). Color coding is as follows: black, RNA positive; blue, RNA negative.\n(C) Dot plot of 2 defining genes for each cell type (Table S1) (Bonferroni-adjusted p \u003c 0.001) and ACE2 and TMPRSS2. Dot size represents fraction of cells within that type expressing a given gene, and color intensity represents binned count-based expression amount (log(scaled UMI+1)) among expressing cells. ACE2 is enriched in type II pneumocytes (6.7% expressing, Bonferroni-adjusted p = 8.62E−33), as is TMPRSS2 (29.5% expressing, Bonferroni-adjusted p = 8.73E−153). Of all type II pneumocytes, 3.8% co-express ACE2 and TMPRSS2 (Table S9). Red arrow indicates cell type with largest proportion of ACE2+TMPRSS2+ cells.\n(D) Genes differentially expressed among ACE2+ and ACE2− type II pneumocytes. (SCDE package, FDR-adjusted p \u003c 0.05 for IFNGR2, NT5DC1, ARL6IP1, and TRIM27; full results can be found in Table S1).\nSee also Table S1."}

LitCovid-PubTator