PMC:7252096 / 47347-50338 JSON TXT

Annnotations TAB JSON ListView MergeView

LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T95","span":{"begin":16,"end":32},"obj":"Body_part"},{"id":"T96","span":{"begin":22,"end":32},"obj":"Body_part"},{"id":"T97","span":{"begin":239,"end":255},"obj":"Body_part"},{"id":"T98","span":{"begin":245,"end":255},"obj":"Body_part"},{"id":"T99","span":{"begin":1285,"end":1289},"obj":"Body_part"},{"id":"T100","span":{"begin":1965,"end":1969},"obj":"Body_part"},{"id":"T101","span":{"begin":2172,"end":2176},"obj":"Body_part"}],"attributes":[{"id":"A95","pred":"uberon_id","subj":"T95","obj":"http://purl.obolibrary.org/obo/UBERON_0005384"},{"id":"A96","pred":"uberon_id","subj":"T96","obj":"http://purl.obolibrary.org/obo/UBERON_0000483"},{"id":"A97","pred":"uberon_id","subj":"T97","obj":"http://purl.obolibrary.org/obo/UBERON_0005384"},{"id":"A98","pred":"uberon_id","subj":"T98","obj":"http://purl.obolibrary.org/obo/UBERON_0000483"},{"id":"A99","pred":"uberon_id","subj":"T99","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A100","pred":"uberon_id","subj":"T100","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A101","pred":"uberon_id","subj":"T101","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"}],"text":"Figure S5 Mouse Nasal Epithelium Following Interferon-α Exposure Related to Figure 6\n(A). Schematic: mice were exposed to 10,000 units of IFN-α or saline by intranasal application (n = 2 per group). After 12 h, animals were sacrificed and nasal epithelium was dissected and dissociated for scRNA-seq using Seq-Well S3.\n(B). Dot plot of 2 defining genes for each cell type, with Ace2, Tmprss2, and Cdhr3. Dot size represents fraction of cells within cell type expressing, and color intensity binned count-based expression level (log(scaled UMI+1)) among expressing cells. All cluster defining genes are provided in Table S8. Red arrows: cell types with largest proportion of Ace2+ cells. Dendrogram (left) by person correlation over differentially expressed genes with Ward clustering.\n(C). UMAP of Basal Epithelial Cells (380 cells) across 4 mice. Black: Saline-treated mouse; red: IFN-α treated.\n(D). UMAP of Basal Epithelial Cells as in C, points colored by detection of Ace2. Black: RNA positive, blue: RNA negative (6.6% Ace2+, Bonferroni-adjusted p = 1.1E-10 for Basal Epithelial Cell expression versus all other cells).\n(E). Schematic: wildtype (WT) and IFNγ-receptor knockout (IFNγR−/−) mice were infected intranasally with murine gamma-herpesvirus-68 (MHV68). Cells from whole lung were digested for scRNA-seq using Drop-seq (yielding 5,558 Epcam+ cells).\n(F). Expression of Ace2 by epithelial cell type, wild type (WT) mice. Statistical significance by Wilcoxon rank sum test with Bonferroni correction.\n(G). Expression of Ace2 among type II pneumocytes binned by infection status in WT mice. All pairwise comparisons non-significant (p \u003e 0.05) by Wilcoxon rank sum test.\n(H). Percent of Ace2+ cells by infection condition (uninfected, bystander cells in MHV68-infected mouse, MHV68 RNA+ cells) and mouse genotype (WT, IFNγR −/−). Black bars: Ace2+ positive cells; white bars: Ace2- cells.\n(I). Schematic of RNA-Seq data from (Matos et al., 2019) of human lung explants (n = 5 donors) exposed to influenza A virus (IAV, H3N2) at 24 h post infection.\n(J). Expression of SFTPC (surfactant protein C, a marker of type II pneumocytes) versus ACE2 among mock-infected lung explants. Statistical significance assessed by Pearson’s correlation, r = 0.93, p = 0.021. TPM: transcripts per million.\n(K). SFTPC expression among matched donors following mock or IAV infection for 24 h. Statistical significance assessed by ratio paired t test, p = 0.86.\n(L). ACE2 expression among matched donors following mock or IAV infection for 24 h. Statistical significance assessed by ratio paired t test, p = 0.0054.\n(M). Western blot of fully-differentiated air-liquid interface cultures from bronchial cells derived from 4 human donors with asthma. Cells from each donor were treated with 10 ng/mL IFNγ for 24 h, and compared to a matched untreated condition. ACE2 protein: AF933 (R\u0026D). Fold changes quantified for IFNγ treated versus untreated for each patient donor following normalization to GAPDH."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T174","span":{"begin":1573,"end":1582},"obj":"Disease"},{"id":"T175","span":{"begin":1712,"end":1721},"obj":"Disease"},{"id":"T176","span":{"begin":2005,"end":2014},"obj":"Disease"},{"id":"T177","span":{"begin":2048,"end":2057},"obj":"Disease"},{"id":"T178","span":{"begin":2363,"end":2372},"obj":"Disease"},{"id":"T179","span":{"begin":2515,"end":2524},"obj":"Disease"},{"id":"T180","span":{"begin":2731,"end":2737},"obj":"Disease"}],"attributes":[{"id":"A174","pred":"mondo_id","subj":"T174","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A175","pred":"mondo_id","subj":"T175","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A176","pred":"mondo_id","subj":"T176","obj":"http://purl.obolibrary.org/obo/MONDO_0005812"},{"id":"A177","pred":"mondo_id","subj":"T177","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A178","pred":"mondo_id","subj":"T178","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A179","pred":"mondo_id","subj":"T179","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A180","pred":"mondo_id","subj":"T180","obj":"http://purl.obolibrary.org/obo/MONDO_0004979"}],"text":"Figure S5 Mouse Nasal Epithelium Following Interferon-α Exposure Related to Figure 6\n(A). Schematic: mice were exposed to 10,000 units of IFN-α or saline by intranasal application (n = 2 per group). After 12 h, animals were sacrificed and nasal epithelium was dissected and dissociated for scRNA-seq using Seq-Well S3.\n(B). Dot plot of 2 defining genes for each cell type, with Ace2, Tmprss2, and Cdhr3. Dot size represents fraction of cells within cell type expressing, and color intensity binned count-based expression level (log(scaled UMI+1)) among expressing cells. All cluster defining genes are provided in Table S8. Red arrows: cell types with largest proportion of Ace2+ cells. Dendrogram (left) by person correlation over differentially expressed genes with Ward clustering.\n(C). UMAP of Basal Epithelial Cells (380 cells) across 4 mice. Black: Saline-treated mouse; red: IFN-α treated.\n(D). UMAP of Basal Epithelial Cells as in C, points colored by detection of Ace2. Black: RNA positive, blue: RNA negative (6.6% Ace2+, Bonferroni-adjusted p = 1.1E-10 for Basal Epithelial Cell expression versus all other cells).\n(E). Schematic: wildtype (WT) and IFNγ-receptor knockout (IFNγR−/−) mice were infected intranasally with murine gamma-herpesvirus-68 (MHV68). Cells from whole lung were digested for scRNA-seq using Drop-seq (yielding 5,558 Epcam+ cells).\n(F). Expression of Ace2 by epithelial cell type, wild type (WT) mice. Statistical significance by Wilcoxon rank sum test with Bonferroni correction.\n(G). Expression of Ace2 among type II pneumocytes binned by infection status in WT mice. All pairwise comparisons non-significant (p \u003e 0.05) by Wilcoxon rank sum test.\n(H). Percent of Ace2+ cells by infection condition (uninfected, bystander cells in MHV68-infected mouse, MHV68 RNA+ cells) and mouse genotype (WT, IFNγR −/−). Black bars: Ace2+ positive cells; white bars: Ace2- cells.\n(I). Schematic of RNA-Seq data from (Matos et al., 2019) of human lung explants (n = 5 donors) exposed to influenza A virus (IAV, H3N2) at 24 h post infection.\n(J). Expression of SFTPC (surfactant protein C, a marker of type II pneumocytes) versus ACE2 among mock-infected lung explants. Statistical significance assessed by Pearson’s correlation, r = 0.93, p = 0.021. TPM: transcripts per million.\n(K). SFTPC expression among matched donors following mock or IAV infection for 24 h. Statistical significance assessed by ratio paired t test, p = 0.86.\n(L). ACE2 expression among matched donors following mock or IAV infection for 24 h. Statistical significance assessed by ratio paired t test, p = 0.0054.\n(M). Western blot of fully-differentiated air-liquid interface cultures from bronchial cells derived from 4 human donors with asthma. Cells from each donor were treated with 10 ng/mL IFNγ for 24 h, and compared to a matched untreated condition. ACE2 protein: AF933 (R\u0026D). Fold changes quantified for IFNγ treated versus untreated for each patient donor following normalization to GAPDH."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-sentences

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T14","span":{"begin":2731,"end":2737},"obj":"Phenotype"}],"attributes":[{"id":"A14","pred":"hp_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/HP_0002099"}],"text":"Figure S5 Mouse Nasal Epithelium Following Interferon-α Exposure Related to Figure 6\n(A). Schematic: mice were exposed to 10,000 units of IFN-α or saline by intranasal application (n = 2 per group). After 12 h, animals were sacrificed and nasal epithelium was dissected and dissociated for scRNA-seq using Seq-Well S3.\n(B). Dot plot of 2 defining genes for each cell type, with Ace2, Tmprss2, and Cdhr3. Dot size represents fraction of cells within cell type expressing, and color intensity binned count-based expression level (log(scaled UMI+1)) among expressing cells. All cluster defining genes are provided in Table S8. Red arrows: cell types with largest proportion of Ace2+ cells. Dendrogram (left) by person correlation over differentially expressed genes with Ward clustering.\n(C). UMAP of Basal Epithelial Cells (380 cells) across 4 mice. Black: Saline-treated mouse; red: IFN-α treated.\n(D). UMAP of Basal Epithelial Cells as in C, points colored by detection of Ace2. Black: RNA positive, blue: RNA negative (6.6% Ace2+, Bonferroni-adjusted p = 1.1E-10 for Basal Epithelial Cell expression versus all other cells).\n(E). Schematic: wildtype (WT) and IFNγ-receptor knockout (IFNγR−/−) mice were infected intranasally with murine gamma-herpesvirus-68 (MHV68). Cells from whole lung were digested for scRNA-seq using Drop-seq (yielding 5,558 Epcam+ cells).\n(F). Expression of Ace2 by epithelial cell type, wild type (WT) mice. Statistical significance by Wilcoxon rank sum test with Bonferroni correction.\n(G). Expression of Ace2 among type II pneumocytes binned by infection status in WT mice. All pairwise comparisons non-significant (p \u003e 0.05) by Wilcoxon rank sum test.\n(H). Percent of Ace2+ cells by infection condition (uninfected, bystander cells in MHV68-infected mouse, MHV68 RNA+ cells) and mouse genotype (WT, IFNγR −/−). Black bars: Ace2+ positive cells; white bars: Ace2- cells.\n(I). Schematic of RNA-Seq data from (Matos et al., 2019) of human lung explants (n = 5 donors) exposed to influenza A virus (IAV, H3N2) at 24 h post infection.\n(J). Expression of SFTPC (surfactant protein C, a marker of type II pneumocytes) versus ACE2 among mock-infected lung explants. Statistical significance assessed by Pearson’s correlation, r = 0.93, p = 0.021. TPM: transcripts per million.\n(K). SFTPC expression among matched donors following mock or IAV infection for 24 h. Statistical significance assessed by ratio paired t test, p = 0.86.\n(L). ACE2 expression among matched donors following mock or IAV infection for 24 h. Statistical significance assessed by ratio paired t test, p = 0.0054.\n(M). Western blot of fully-differentiated air-liquid interface cultures from bronchial cells derived from 4 human donors with asthma. Cells from each donor were treated with 10 ng/mL IFNγ for 24 h, and compared to a matched untreated condition. ACE2 protein: AF933 (R\u0026D). Fold changes quantified for IFNγ treated versus untreated for each patient donor following normalization to GAPDH."}

LitCovid-PubTator

2_test

{"project":"2_test","denotations":[{"id":"32413319-31826721-20790494","span":{"begin":1950,"end":1954},"obj":"31826721"}],"text":"Figure S5 Mouse Nasal Epithelium Following Interferon-α Exposure Related to Figure 6\n(A). Schematic: mice were exposed to 10,000 units of IFN-α or saline by intranasal application (n = 2 per group). After 12 h, animals were sacrificed and nasal epithelium was dissected and dissociated for scRNA-seq using Seq-Well S3.\n(B). Dot plot of 2 defining genes for each cell type, with Ace2, Tmprss2, and Cdhr3. Dot size represents fraction of cells within cell type expressing, and color intensity binned count-based expression level (log(scaled UMI+1)) among expressing cells. All cluster defining genes are provided in Table S8. Red arrows: cell types with largest proportion of Ace2+ cells. Dendrogram (left) by person correlation over differentially expressed genes with Ward clustering.\n(C). UMAP of Basal Epithelial Cells (380 cells) across 4 mice. Black: Saline-treated mouse; red: IFN-α treated.\n(D). UMAP of Basal Epithelial Cells as in C, points colored by detection of Ace2. Black: RNA positive, blue: RNA negative (6.6% Ace2+, Bonferroni-adjusted p = 1.1E-10 for Basal Epithelial Cell expression versus all other cells).\n(E). Schematic: wildtype (WT) and IFNγ-receptor knockout (IFNγR−/−) mice were infected intranasally with murine gamma-herpesvirus-68 (MHV68). Cells from whole lung were digested for scRNA-seq using Drop-seq (yielding 5,558 Epcam+ cells).\n(F). Expression of Ace2 by epithelial cell type, wild type (WT) mice. Statistical significance by Wilcoxon rank sum test with Bonferroni correction.\n(G). Expression of Ace2 among type II pneumocytes binned by infection status in WT mice. All pairwise comparisons non-significant (p \u003e 0.05) by Wilcoxon rank sum test.\n(H). Percent of Ace2+ cells by infection condition (uninfected, bystander cells in MHV68-infected mouse, MHV68 RNA+ cells) and mouse genotype (WT, IFNγR −/−). Black bars: Ace2+ positive cells; white bars: Ace2- cells.\n(I). Schematic of RNA-Seq data from (Matos et al., 2019) of human lung explants (n = 5 donors) exposed to influenza A virus (IAV, H3N2) at 24 h post infection.\n(J). Expression of SFTPC (surfactant protein C, a marker of type II pneumocytes) versus ACE2 among mock-infected lung explants. Statistical significance assessed by Pearson’s correlation, r = 0.93, p = 0.021. TPM: transcripts per million.\n(K). SFTPC expression among matched donors following mock or IAV infection for 24 h. Statistical significance assessed by ratio paired t test, p = 0.86.\n(L). ACE2 expression among matched donors following mock or IAV infection for 24 h. Statistical significance assessed by ratio paired t test, p = 0.0054.\n(M). Western blot of fully-differentiated air-liquid interface cultures from bronchial cells derived from 4 human donors with asthma. Cells from each donor were treated with 10 ng/mL IFNγ for 24 h, and compared to a matched untreated condition. ACE2 protein: AF933 (R\u0026D). Fold changes quantified for IFNγ treated versus untreated for each patient donor following normalization to GAPDH."}

PMC:7252096 / 47347-50338 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7252096 / 47347-50338 JSON TXT