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LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T49","span":{"begin":217,"end":222},"obj":"Body_part"}],"attributes":[{"id":"A49","pred":"uberon_id","subj":"T49","obj":"http://purl.obolibrary.org/obo/UBERON_0002116"}],"text":"Figure 3 NHP and Human Ileal Absorptive Enterocytes Co-Express ACE2 and TMPRSS2\n(A) Expression ACE2 across diverse tissues in healthy NHPs (n = 3 animals; 52,858 cells).\n(B) Schematic of protocol for isolation of NHP ileum (n = 5) at necropsy for scRNA-seq using Seq-Well v1, and computational pipeline to identify cell types by using unbiased methods. Shown on the right is a UMAP projection of 4,515 cells colored by cell type.\n(C) Dot plot of 2 defining genes for each cell type, with ACE2 and TMPRSS2. Dot size represents fraction of cells within cell type expressing a given gene, and color intensity represents binned count-based expression amounts (log(scaled UMI+1)) among expressing cells. All cluster defining genes are provided in Table S4. Red arrow indicates cell type with largest proportion of ACE2+TMPRSS2+ cells.\n(D) Schematic of protocol for isolation of human ileal cells from endoscopic pinch biopsies in non-inflamed regions (n = 13). Shown on the right is a tSNE plot of 13,689 epithelial cells selected from original dataset generated by 10x 3′ v2 (see Figure S2), colored by cellular subsets.\n(E). Dot plot of 2 defining genes for each cell type, with ACE2 and TMPRSS2. Dot size represents fraction of cells within cell type expressing a given gene, and color intensity represents binned count-based expression amounts (log(scaled UMI+1)) among expressing cells. All cluster defining genes are provided in Table S5. Red arrow indicates cell type with largest proportion of ACE2+TMPRSS2+ cells.\n(F). Expression of ACE2 (left) and TMPRSS2 (right) among all epithelial subsets from human donors.\nSee also Figure S2 and Tables S4 and S5."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T87","span":{"begin":52,"end":54},"obj":"Chemical"},{"id":"T88","span":{"begin":748,"end":750},"obj":"Chemical"},{"id":"T89","span":{"begin":1083,"end":1085},"obj":"Chemical"},{"id":"T90","span":{"begin":1436,"end":1438},"obj":"Chemical"},{"id":"T91","span":{"begin":1633,"end":1635},"obj":"Chemical"},{"id":"T92","span":{"begin":1647,"end":1649},"obj":"Chemical"},{"id":"T93","span":{"begin":1654,"end":1656},"obj":"Chemical"}],"attributes":[{"id":"A87","pred":"chebi_id","subj":"T87","obj":"http://purl.obolibrary.org/obo/CHEBI_27638"},{"id":"A88","pred":"chebi_id","subj":"T88","obj":"http://purl.obolibrary.org/obo/CHEBI_29401"},{"id":"A89","pred":"chebi_id","subj":"T89","obj":"http://purl.obolibrary.org/obo/CHEBI_29387"},{"id":"A90","pred":"chebi_id","subj":"T90","obj":"http://purl.obolibrary.org/obo/CHEBI_29386"},{"id":"A91","pred":"chebi_id","subj":"T91","obj":"http://purl.obolibrary.org/obo/CHEBI_29387"},{"id":"A92","pred":"chebi_id","subj":"T92","obj":"http://purl.obolibrary.org/obo/CHEBI_29401"},{"id":"A93","pred":"chebi_id","subj":"T93","obj":"http://purl.obolibrary.org/obo/CHEBI_29386"}],"text":"Figure 3 NHP and Human Ileal Absorptive Enterocytes Co-Express ACE2 and TMPRSS2\n(A) Expression ACE2 across diverse tissues in healthy NHPs (n = 3 animals; 52,858 cells).\n(B) Schematic of protocol for isolation of NHP ileum (n = 5) at necropsy for scRNA-seq using Seq-Well v1, and computational pipeline to identify cell types by using unbiased methods. Shown on the right is a UMAP projection of 4,515 cells colored by cell type.\n(C) Dot plot of 2 defining genes for each cell type, with ACE2 and TMPRSS2. Dot size represents fraction of cells within cell type expressing a given gene, and color intensity represents binned count-based expression amounts (log(scaled UMI+1)) among expressing cells. All cluster defining genes are provided in Table S4. Red arrow indicates cell type with largest proportion of ACE2+TMPRSS2+ cells.\n(D) Schematic of protocol for isolation of human ileal cells from endoscopic pinch biopsies in non-inflamed regions (n = 13). Shown on the right is a tSNE plot of 13,689 epithelial cells selected from original dataset generated by 10x 3′ v2 (see Figure S2), colored by cellular subsets.\n(E). Dot plot of 2 defining genes for each cell type, with ACE2 and TMPRSS2. Dot size represents fraction of cells within cell type expressing a given gene, and color intensity represents binned count-based expression amounts (log(scaled UMI+1)) among expressing cells. All cluster defining genes are provided in Table S5. Red arrow indicates cell type with largest proportion of ACE2+TMPRSS2+ cells.\n(F). Expression of ACE2 (left) and TMPRSS2 (right) among all epithelial subsets from human donors.\nSee also Figure S2 and Tables S4 and S5."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T132","span":{"begin":0,"end":79},"obj":"Sentence"},{"id":"T133","span":{"begin":80,"end":169},"obj":"Sentence"},{"id":"T134","span":{"begin":170,"end":352},"obj":"Sentence"},{"id":"T135","span":{"begin":353,"end":429},"obj":"Sentence"},{"id":"T136","span":{"begin":430,"end":505},"obj":"Sentence"},{"id":"T137","span":{"begin":506,"end":698},"obj":"Sentence"},{"id":"T138","span":{"begin":699,"end":751},"obj":"Sentence"},{"id":"T139","span":{"begin":752,"end":829},"obj":"Sentence"},{"id":"T140","span":{"begin":830,"end":955},"obj":"Sentence"},{"id":"T141","span":{"begin":956,"end":1116},"obj":"Sentence"},{"id":"T142","span":{"begin":1117,"end":1121},"obj":"Sentence"},{"id":"T143","span":{"begin":1122,"end":1193},"obj":"Sentence"},{"id":"T144","span":{"begin":1194,"end":1386},"obj":"Sentence"},{"id":"T145","span":{"begin":1387,"end":1439},"obj":"Sentence"},{"id":"T146","span":{"begin":1440,"end":1517},"obj":"Sentence"},{"id":"T147","span":{"begin":1518,"end":1522},"obj":"Sentence"},{"id":"T148","span":{"begin":1523,"end":1616},"obj":"Sentence"},{"id":"T149","span":{"begin":1617,"end":1657},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Figure 3 NHP and Human Ileal Absorptive Enterocytes Co-Express ACE2 and TMPRSS2\n(A) Expression ACE2 across diverse tissues in healthy NHPs (n = 3 animals; 52,858 cells).\n(B) Schematic of protocol for isolation of NHP ileum (n = 5) at necropsy for scRNA-seq using Seq-Well v1, and computational pipeline to identify cell types by using unbiased methods. Shown on the right is a UMAP projection of 4,515 cells colored by cell type.\n(C) Dot plot of 2 defining genes for each cell type, with ACE2 and TMPRSS2. Dot size represents fraction of cells within cell type expressing a given gene, and color intensity represents binned count-based expression amounts (log(scaled UMI+1)) among expressing cells. All cluster defining genes are provided in Table S4. Red arrow indicates cell type with largest proportion of ACE2+TMPRSS2+ cells.\n(D) Schematic of protocol for isolation of human ileal cells from endoscopic pinch biopsies in non-inflamed regions (n = 13). Shown on the right is a tSNE plot of 13,689 epithelial cells selected from original dataset generated by 10x 3′ v2 (see Figure S2), colored by cellular subsets.\n(E). Dot plot of 2 defining genes for each cell type, with ACE2 and TMPRSS2. Dot size represents fraction of cells within cell type expressing a given gene, and color intensity represents binned count-based expression amounts (log(scaled UMI+1)) among expressing cells. All cluster defining genes are provided in Table S5. Red arrow indicates cell type with largest proportion of ACE2+TMPRSS2+ cells.\n(F). Expression of ACE2 (left) and TMPRSS2 (right) among all epithelial subsets from human donors.\nSee also Figure S2 and Tables S4 and S5."}

LitCovid-PubTator

{"project":"LitCovid-PubTator","denotations":[{"id":"618","span":{"begin":63,"end":67},"obj":"Gene"},{"id":"619","span":{"begin":17,"end":22},"obj":"Species"},{"id":"621","span":{"begin":95,"end":99},"obj":"Gene"},{"id":"626","span":{"begin":488,"end":492},"obj":"Gene"},{"id":"627","span":{"begin":497,"end":504},"obj":"Gene"},{"id":"628","span":{"begin":809,"end":813},"obj":"Gene"},{"id":"629","span":{"begin":814,"end":821},"obj":"Gene"},{"id":"631","span":{"begin":873,"end":878},"obj":"Species"},{"id":"636","span":{"begin":1176,"end":1180},"obj":"Gene"},{"id":"637","span":{"begin":1185,"end":1192},"obj":"Gene"},{"id":"638","span":{"begin":1497,"end":1501},"obj":"Gene"},{"id":"639","span":{"begin":1502,"end":1509},"obj":"Gene"},{"id":"643","span":{"begin":1537,"end":1541},"obj":"Gene"},{"id":"644","span":{"begin":1553,"end":1560},"obj":"Gene"},{"id":"645","span":{"begin":1603,"end":1608},"obj":"Species"}],"attributes":[{"id":"A618","pred":"tao:has_database_id","subj":"618","obj":"Gene:59272"},{"id":"A619","pred":"tao:has_database_id","subj":"619","obj":"Tax:9606"},{"id":"A621","pred":"tao:has_database_id","subj":"621","obj":"Gene:59272"},{"id":"A626","pred":"tao:has_database_id","subj":"626","obj":"Gene:59272"},{"id":"A627","pred":"tao:has_database_id","subj":"627","obj":"Gene:7113"},{"id":"A628","pred":"tao:has_database_id","subj":"628","obj":"Gene:59272"},{"id":"A629","pred":"tao:has_database_id","subj":"629","obj":"Gene:7113"},{"id":"A631","pred":"tao:has_database_id","subj":"631","obj":"Tax:9606"},{"id":"A636","pred":"tao:has_database_id","subj":"636","obj":"Gene:59272"},{"id":"A637","pred":"tao:has_database_id","subj":"637","obj":"Gene:7113"},{"id":"A638","pred":"tao:has_database_id","subj":"638","obj":"Gene:59272"},{"id":"A639","pred":"tao:has_database_id","subj":"639","obj":"Gene:7113"},{"id":"A643","pred":"tao:has_database_id","subj":"643","obj":"Gene:59272"},{"id":"A644","pred":"tao:has_database_id","subj":"644","obj":"Gene:7113"},{"id":"A645","pred":"tao:has_database_id","subj":"645","obj":"Tax:9606"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"Figure 3 NHP and Human Ileal Absorptive Enterocytes Co-Express ACE2 and TMPRSS2\n(A) Expression ACE2 across diverse tissues in healthy NHPs (n = 3 animals; 52,858 cells).\n(B) Schematic of protocol for isolation of NHP ileum (n = 5) at necropsy for scRNA-seq using Seq-Well v1, and computational pipeline to identify cell types by using unbiased methods. Shown on the right is a UMAP projection of 4,515 cells colored by cell type.\n(C) Dot plot of 2 defining genes for each cell type, with ACE2 and TMPRSS2. Dot size represents fraction of cells within cell type expressing a given gene, and color intensity represents binned count-based expression amounts (log(scaled UMI+1)) among expressing cells. All cluster defining genes are provided in Table S4. Red arrow indicates cell type with largest proportion of ACE2+TMPRSS2+ cells.\n(D) Schematic of protocol for isolation of human ileal cells from endoscopic pinch biopsies in non-inflamed regions (n = 13). Shown on the right is a tSNE plot of 13,689 epithelial cells selected from original dataset generated by 10x 3′ v2 (see Figure S2), colored by cellular subsets.\n(E). Dot plot of 2 defining genes for each cell type, with ACE2 and TMPRSS2. Dot size represents fraction of cells within cell type expressing a given gene, and color intensity represents binned count-based expression amounts (log(scaled UMI+1)) among expressing cells. All cluster defining genes are provided in Table S5. Red arrow indicates cell type with largest proportion of ACE2+TMPRSS2+ cells.\n(F). Expression of ACE2 (left) and TMPRSS2 (right) among all epithelial subsets from human donors.\nSee also Figure S2 and Tables S4 and S5."}