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LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T30","span":{"begin":7,"end":11},"obj":"Body_part"},{"id":"T31","span":{"begin":189,"end":193},"obj":"Body_part"},{"id":"T32","span":{"begin":194,"end":200},"obj":"Body_part"}],"attributes":[{"id":"A30","pred":"uberon_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A31","pred":"uberon_id","subj":"T31","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A32","pred":"uberon_id","subj":"T32","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"}],"text":"Select Lung Epithelial Cells from Control, HIV-1-Infected, and Mycobacterium-tuberculosis-Infected Human Donors Co-Express ACE2 and TMPRSS2\n(A) Schematic of protocol for isolation of human lung tissue from surgical excess, creation of scRNA-seq libraries by using Seq-Well S3, and computational analysis to identify cell types by using unbiased methods. Shown on the right is a UMAP projection of 18,915 cells across 8 donors (n = 3 TB+HIV+; n = 3 TB+; n = 2 non-infected patients). Cells represented by points, colored according to cell type (see STAR Methods).\n(B) UMAP projection as in (A), points colored by detection of ACE2 (top) or TMPRSS2 (bottom). Color coding is as follows: black, RNA positive; blue, RNA negative.\n(C) Dot plot of 2 defining genes for each cell type (FDR-adjusted p \u003c 0.001), and ACE2 and TMPRSS2; dot size represents fraction of cells within cell type expressing a given gene, and color intensity represents binned count-based expression amount (log(scaled UMI+1)) among expressing cells. All cluster-defining genes are provided in Table S2. Red arrow indicates cell types with largest proportion of ACE2+TMPRSS2+ cells.\n(D) Volcano plot identifying significantly upregulated genes in ACE2+TMPRSS2+ pneumocytes compared with all remaining pneumocytes. Red points represent genes with a FDR-adjusted p \u003c 0.05, and log2(fold change) \u003e1.5. Text highlighting specific genes; the full list is available in Table S2.\n(E) Expression of ACE2 across human donors by HIV and TB status (p = 0.009 by likelihood-ratio test).\nSee also Table S2."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T92","span":{"begin":77,"end":89},"obj":"Disease"},{"id":"T93","span":{"begin":433,"end":435},"obj":"Disease"},{"id":"T94","span":{"begin":448,"end":450},"obj":"Disease"},{"id":"T95","span":{"begin":548,"end":552},"obj":"Disease"},{"id":"T96","span":{"begin":1494,"end":1496},"obj":"Disease"}],"attributes":[{"id":"A92","pred":"mondo_id","subj":"T92","obj":"http://purl.obolibrary.org/obo/MONDO_0018076"},{"id":"A93","pred":"mondo_id","subj":"T93","obj":"http://purl.obolibrary.org/obo/MONDO_0018076"},{"id":"A94","pred":"mondo_id","subj":"T94","obj":"http://purl.obolibrary.org/obo/MONDO_0018076"},{"id":"A95","pred":"mondo_id","subj":"T95","obj":"http://purl.obolibrary.org/obo/MONDO_0010408"},{"id":"A96","pred":"mondo_id","subj":"T96","obj":"http://purl.obolibrary.org/obo/MONDO_0018076"}],"text":"Select Lung Epithelial Cells from Control, HIV-1-Infected, and Mycobacterium-tuberculosis-Infected Human Donors Co-Express ACE2 and TMPRSS2\n(A) Schematic of protocol for isolation of human lung tissue from surgical excess, creation of scRNA-seq libraries by using Seq-Well S3, and computational analysis to identify cell types by using unbiased methods. Shown on the right is a UMAP projection of 18,915 cells across 8 donors (n = 3 TB+HIV+; n = 3 TB+; n = 2 non-infected patients). Cells represented by points, colored according to cell type (see STAR Methods).\n(B) UMAP projection as in (A), points colored by detection of ACE2 (top) or TMPRSS2 (bottom). Color coding is as follows: black, RNA positive; blue, RNA negative.\n(C) Dot plot of 2 defining genes for each cell type (FDR-adjusted p \u003c 0.001), and ACE2 and TMPRSS2; dot size represents fraction of cells within cell type expressing a given gene, and color intensity represents binned count-based expression amount (log(scaled UMI+1)) among expressing cells. All cluster-defining genes are provided in Table S2. Red arrow indicates cell types with largest proportion of ACE2+TMPRSS2+ cells.\n(D) Volcano plot identifying significantly upregulated genes in ACE2+TMPRSS2+ pneumocytes compared with all remaining pneumocytes. Red points represent genes with a FDR-adjusted p \u003c 0.05, and log2(fold change) \u003e1.5. Text highlighting specific genes; the full list is available in Table S2.\n(E) Expression of ACE2 across human donors by HIV and TB status (p = 0.009 by likelihood-ratio test).\nSee also Table S2."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T59","span":{"begin":112,"end":114},"obj":"Chemical"},{"id":"T60","span":{"begin":273,"end":275},"obj":"Chemical"},{"id":"T61","span":{"begin":1067,"end":1069},"obj":"Chemical"},{"id":"T62","span":{"begin":1436,"end":1438},"obj":"Chemical"},{"id":"T63","span":{"begin":1557,"end":1559},"obj":"Chemical"}],"attributes":[{"id":"A59","pred":"chebi_id","subj":"T59","obj":"http://purl.obolibrary.org/obo/CHEBI_27638"},{"id":"A60","pred":"chebi_id","subj":"T60","obj":"http://purl.obolibrary.org/obo/CHEBI_29388"},{"id":"A61","pred":"chebi_id","subj":"T61","obj":"http://purl.obolibrary.org/obo/CHEBI_29387"},{"id":"A62","pred":"chebi_id","subj":"T62","obj":"http://purl.obolibrary.org/obo/CHEBI_29387"},{"id":"A63","pred":"chebi_id","subj":"T63","obj":"http://purl.obolibrary.org/obo/CHEBI_29387"}],"text":"Select Lung Epithelial Cells from Control, HIV-1-Infected, and Mycobacterium-tuberculosis-Infected Human Donors Co-Express ACE2 and TMPRSS2\n(A) Schematic of protocol for isolation of human lung tissue from surgical excess, creation of scRNA-seq libraries by using Seq-Well S3, and computational analysis to identify cell types by using unbiased methods. Shown on the right is a UMAP projection of 18,915 cells across 8 donors (n = 3 TB+HIV+; n = 3 TB+; n = 2 non-infected patients). Cells represented by points, colored according to cell type (see STAR Methods).\n(B) UMAP projection as in (A), points colored by detection of ACE2 (top) or TMPRSS2 (bottom). Color coding is as follows: black, RNA positive; blue, RNA negative.\n(C) Dot plot of 2 defining genes for each cell type (FDR-adjusted p \u003c 0.001), and ACE2 and TMPRSS2; dot size represents fraction of cells within cell type expressing a given gene, and color intensity represents binned count-based expression amount (log(scaled UMI+1)) among expressing cells. All cluster-defining genes are provided in Table S2. Red arrow indicates cell types with largest proportion of ACE2+TMPRSS2+ cells.\n(D) Volcano plot identifying significantly upregulated genes in ACE2+TMPRSS2+ pneumocytes compared with all remaining pneumocytes. Red points represent genes with a FDR-adjusted p \u003c 0.05, and log2(fold change) \u003e1.5. Text highlighting specific genes; the full list is available in Table S2.\n(E) Expression of ACE2 across human donors by HIV and TB status (p = 0.009 by likelihood-ratio test).\nSee also Table S2."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T86","span":{"begin":140,"end":353},"obj":"Sentence"},{"id":"T87","span":{"begin":354,"end":482},"obj":"Sentence"},{"id":"T88","span":{"begin":483,"end":562},"obj":"Sentence"},{"id":"T89","span":{"begin":563,"end":656},"obj":"Sentence"},{"id":"T90","span":{"begin":657,"end":725},"obj":"Sentence"},{"id":"T91","span":{"begin":726,"end":1017},"obj":"Sentence"},{"id":"T92","span":{"begin":1018,"end":1070},"obj":"Sentence"},{"id":"T93","span":{"begin":1071,"end":1149},"obj":"Sentence"},{"id":"T94","span":{"begin":1150,"end":1280},"obj":"Sentence"},{"id":"T95","span":{"begin":1281,"end":1365},"obj":"Sentence"},{"id":"T96","span":{"begin":1366,"end":1439},"obj":"Sentence"},{"id":"T97","span":{"begin":1440,"end":1541},"obj":"Sentence"},{"id":"T98","span":{"begin":1542,"end":1560},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Select Lung Epithelial Cells from Control, HIV-1-Infected, and Mycobacterium-tuberculosis-Infected Human Donors Co-Express ACE2 and TMPRSS2\n(A) Schematic of protocol for isolation of human lung tissue from surgical excess, creation of scRNA-seq libraries by using Seq-Well S3, and computational analysis to identify cell types by using unbiased methods. Shown on the right is a UMAP projection of 18,915 cells across 8 donors (n = 3 TB+HIV+; n = 3 TB+; n = 2 non-infected patients). Cells represented by points, colored according to cell type (see STAR Methods).\n(B) UMAP projection as in (A), points colored by detection of ACE2 (top) or TMPRSS2 (bottom). Color coding is as follows: black, RNA positive; blue, RNA negative.\n(C) Dot plot of 2 defining genes for each cell type (FDR-adjusted p \u003c 0.001), and ACE2 and TMPRSS2; dot size represents fraction of cells within cell type expressing a given gene, and color intensity represents binned count-based expression amount (log(scaled UMI+1)) among expressing cells. All cluster-defining genes are provided in Table S2. Red arrow indicates cell types with largest proportion of ACE2+TMPRSS2+ cells.\n(D) Volcano plot identifying significantly upregulated genes in ACE2+TMPRSS2+ pneumocytes compared with all remaining pneumocytes. Red points represent genes with a FDR-adjusted p \u003c 0.05, and log2(fold change) \u003e1.5. Text highlighting specific genes; the full list is available in Table S2.\n(E) Expression of ACE2 across human donors by HIV and TB status (p = 0.009 by likelihood-ratio test).\nSee also Table S2."}

LitCovid-PubTator