PMC:7574920 / 13111-14325 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T73","span":{"begin":101,"end":104},"obj":"Body_part"},{"id":"T74","span":{"begin":546,"end":550},"obj":"Body_part"}],"attributes":[{"id":"A73","pred":"fma_id","subj":"T73","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A74","pred":"fma_id","subj":"T74","obj":"http://purl.org/sig/ont/fma/fma74402"}],"text":"Fig. 2 Sensitivity and specificity of the RT-LAMP assay compared to RT-qPCR using clinical samples.\nRNA samples isolated from 95 pharyngeal swab specimens were analyzed by the RT-LAMP assay using a 96-well plate. The RT-LAMP reaction was incubated at 65°C, and the incubation was interrupted at different time points by cooling on ice for 30 s. (A) Photograph of the 96-well plate after a 30-min incubation at 65°C, taken with a mobile phone. Wells with a yellow color indicate successful RT-LAMP amplification of a fragment of the SARS-CoV-2 N gene (using the N-A primer set). (B) Quantification of the red-to-yellow color change in all wells using spectrophotometric OD measurements. The color value at the given time points is quantified as the difference between the wavelengths of the two absorbance maxima of phenol red: ΔOD = OD434 nm – OD560 nm. Yellow (positive) samples yield a ΔOD of about 0.3 to 0.4. Each line represents one sample. For each sample, the line color indicates the CT (cycle threshold) value obtained from RT-qPCR data (using the E-Sarbeco primers) (15). (C) Scatter plot of ΔOD values at the 30-min time point from (B) compared to CT values from RT-qPCR. Each dot is one sample (well)."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T52","span":{"begin":533,"end":541},"obj":"Disease"},{"id":"T53","span":{"begin":670,"end":672},"obj":"Disease"},{"id":"T54","span":{"begin":829,"end":831},"obj":"Disease"},{"id":"T55","span":{"begin":890,"end":892},"obj":"Disease"},{"id":"T56","span":{"begin":1104,"end":1106},"obj":"Disease"}],"attributes":[{"id":"A52","pred":"mondo_id","subj":"T52","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A53","pred":"mondo_id","subj":"T53","obj":"http://purl.obolibrary.org/obo/MONDO_0017178"},{"id":"A54","pred":"mondo_id","subj":"T54","obj":"http://purl.obolibrary.org/obo/MONDO_0017178"},{"id":"A55","pred":"mondo_id","subj":"T55","obj":"http://purl.obolibrary.org/obo/MONDO_0017178"},{"id":"A56","pred":"mondo_id","subj":"T56","obj":"http://purl.obolibrary.org/obo/MONDO_0017178"}],"text":"Fig. 2 Sensitivity and specificity of the RT-LAMP assay compared to RT-qPCR using clinical samples.\nRNA samples isolated from 95 pharyngeal swab specimens were analyzed by the RT-LAMP assay using a 96-well plate. The RT-LAMP reaction was incubated at 65°C, and the incubation was interrupted at different time points by cooling on ice for 30 s. (A) Photograph of the 96-well plate after a 30-min incubation at 65°C, taken with a mobile phone. Wells with a yellow color indicate successful RT-LAMP amplification of a fragment of the SARS-CoV-2 N gene (using the N-A primer set). (B) Quantification of the red-to-yellow color change in all wells using spectrophotometric OD measurements. The color value at the given time points is quantified as the difference between the wavelengths of the two absorbance maxima of phenol red: ΔOD = OD434 nm – OD560 nm. Yellow (positive) samples yield a ΔOD of about 0.3 to 0.4. Each line represents one sample. For each sample, the line color indicates the CT (cycle threshold) value obtained from RT-qPCR data (using the E-Sarbeco primers) (15). (C) Scatter plot of ΔOD values at the 30-min time point from (B) compared to CT values from RT-qPCR. Each dot is one sample (well)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T125","span":{"begin":197,"end":198},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T126","span":{"begin":347,"end":348},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T127","span":{"begin":388,"end":389},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T128","span":{"begin":428,"end":429},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T129","span":{"begin":455,"end":456},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T130","span":{"begin":515,"end":516},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T131","span":{"begin":546,"end":550},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T132","span":{"begin":564,"end":565},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T133","span":{"begin":580,"end":581},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T134","span":{"begin":887,"end":888},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T135","span":{"begin":1145,"end":1146},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"}],"text":"Fig. 2 Sensitivity and specificity of the RT-LAMP assay compared to RT-qPCR using clinical samples.\nRNA samples isolated from 95 pharyngeal swab specimens were analyzed by the RT-LAMP assay using a 96-well plate. The RT-LAMP reaction was incubated at 65°C, and the incubation was interrupted at different time points by cooling on ice for 30 s. (A) Photograph of the 96-well plate after a 30-min incubation at 65°C, taken with a mobile phone. Wells with a yellow color indicate successful RT-LAMP amplification of a fragment of the SARS-CoV-2 N gene (using the N-A primer set). (B) Quantification of the red-to-yellow color change in all wells using spectrophotometric OD measurements. The color value at the given time points is quantified as the difference between the wavelengths of the two absorbance maxima of phenol red: ΔOD = OD434 nm – OD560 nm. Yellow (positive) samples yield a ΔOD of about 0.3 to 0.4. Each line represents one sample. For each sample, the line color indicates the CT (cycle threshold) value obtained from RT-qPCR data (using the E-Sarbeco primers) (15). (C) Scatter plot of ΔOD values at the 30-min time point from (B) compared to CT values from RT-qPCR. Each dot is one sample (well)."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T46","span":{"begin":816,"end":826},"obj":"Chemical"},{"id":"T47","span":{"begin":816,"end":822},"obj":"Chemical"}],"attributes":[{"id":"A46","pred":"chebi_id","subj":"T46","obj":"http://purl.obolibrary.org/obo/CHEBI_31991"},{"id":"A47","pred":"chebi_id","subj":"T47","obj":"http://purl.obolibrary.org/obo/CHEBI_15882"}],"text":"Fig. 2 Sensitivity and specificity of the RT-LAMP assay compared to RT-qPCR using clinical samples.\nRNA samples isolated from 95 pharyngeal swab specimens were analyzed by the RT-LAMP assay using a 96-well plate. The RT-LAMP reaction was incubated at 65°C, and the incubation was interrupted at different time points by cooling on ice for 30 s. (A) Photograph of the 96-well plate after a 30-min incubation at 65°C, taken with a mobile phone. Wells with a yellow color indicate successful RT-LAMP amplification of a fragment of the SARS-CoV-2 N gene (using the N-A primer set). (B) Quantification of the red-to-yellow color change in all wells using spectrophotometric OD measurements. The color value at the given time points is quantified as the difference between the wavelengths of the two absorbance maxima of phenol red: ΔOD = OD434 nm – OD560 nm. Yellow (positive) samples yield a ΔOD of about 0.3 to 0.4. Each line represents one sample. For each sample, the line color indicates the CT (cycle threshold) value obtained from RT-qPCR data (using the E-Sarbeco primers) (15). (C) Scatter plot of ΔOD values at the 30-min time point from (B) compared to CT values from RT-qPCR. Each dot is one sample (well)."}

{"project":"LitCovid-PubTator","denotations":[{"id":"164","span":{"begin":544,"end":545},"obj":"Gene"},{"id":"165","span":{"begin":562,"end":563},"obj":"Gene"},{"id":"166","span":{"begin":533,"end":543},"obj":"Species"},{"id":"167","span":{"begin":816,"end":826},"obj":"Chemical"}],"attributes":[{"id":"A164","pred":"tao:has_database_id","subj":"164","obj":"Gene:43740575"},{"id":"A165","pred":"tao:has_database_id","subj":"165","obj":"Gene:43740575"},{"id":"A166","pred":"tao:has_database_id","subj":"166","obj":"Tax:2697049"},{"id":"A167","pred":"tao:has_database_id","subj":"167","obj":"MESH:D010637"}],"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":"Fig. 2 Sensitivity and specificity of the RT-LAMP assay compared to RT-qPCR using clinical samples.\nRNA samples isolated from 95 pharyngeal swab specimens were analyzed by the RT-LAMP assay using a 96-well plate. The RT-LAMP reaction was incubated at 65°C, and the incubation was interrupted at different time points by cooling on ice for 30 s. (A) Photograph of the 96-well plate after a 30-min incubation at 65°C, taken with a mobile phone. Wells with a yellow color indicate successful RT-LAMP amplification of a fragment of the SARS-CoV-2 N gene (using the N-A primer set). (B) Quantification of the red-to-yellow color change in all wells using spectrophotometric OD measurements. The color value at the given time points is quantified as the difference between the wavelengths of the two absorbance maxima of phenol red: ΔOD = OD434 nm – OD560 nm. Yellow (positive) samples yield a ΔOD of about 0.3 to 0.4. Each line represents one sample. For each sample, the line color indicates the CT (cycle threshold) value obtained from RT-qPCR data (using the E-Sarbeco primers) (15). (C) Scatter plot of ΔOD values at the 30-min time point from (B) compared to CT values from RT-qPCR. Each dot is one sample (well)."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T69","span":{"begin":43,"end":45},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T70","span":{"begin":69,"end":71},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T71","span":{"begin":177,"end":179},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T72","span":{"begin":218,"end":220},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T73","span":{"begin":490,"end":492},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T74","span":{"begin":1034,"end":1036},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T75","span":{"begin":1175,"end":1177},"obj":"http://purl.obolibrary.org/obo/GO_0001171"}],"text":"Fig. 2 Sensitivity and specificity of the RT-LAMP assay compared to RT-qPCR using clinical samples.\nRNA samples isolated from 95 pharyngeal swab specimens were analyzed by the RT-LAMP assay using a 96-well plate. The RT-LAMP reaction was incubated at 65°C, and the incubation was interrupted at different time points by cooling on ice for 30 s. (A) Photograph of the 96-well plate after a 30-min incubation at 65°C, taken with a mobile phone. Wells with a yellow color indicate successful RT-LAMP amplification of a fragment of the SARS-CoV-2 N gene (using the N-A primer set). (B) Quantification of the red-to-yellow color change in all wells using spectrophotometric OD measurements. The color value at the given time points is quantified as the difference between the wavelengths of the two absorbance maxima of phenol red: ΔOD = OD434 nm – OD560 nm. Yellow (positive) samples yield a ΔOD of about 0.3 to 0.4. Each line represents one sample. For each sample, the line color indicates the CT (cycle threshold) value obtained from RT-qPCR data (using the E-Sarbeco primers) (15). (C) Scatter plot of ΔOD values at the 30-min time point from (B) compared to CT values from RT-qPCR. Each dot is one sample (well)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T83","span":{"begin":0,"end":100},"obj":"Sentence"},{"id":"T84","span":{"begin":101,"end":213},"obj":"Sentence"},{"id":"T85","span":{"begin":214,"end":443},"obj":"Sentence"},{"id":"T86","span":{"begin":444,"end":686},"obj":"Sentence"},{"id":"T87","span":{"begin":687,"end":854},"obj":"Sentence"},{"id":"T88","span":{"begin":855,"end":913},"obj":"Sentence"},{"id":"T89","span":{"begin":914,"end":946},"obj":"Sentence"},{"id":"T90","span":{"begin":947,"end":1183},"obj":"Sentence"},{"id":"T91","span":{"begin":1184,"end":1214},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Fig. 2 Sensitivity and specificity of the RT-LAMP assay compared to RT-qPCR using clinical samples.\nRNA samples isolated from 95 pharyngeal swab specimens were analyzed by the RT-LAMP assay using a 96-well plate. The RT-LAMP reaction was incubated at 65°C, and the incubation was interrupted at different time points by cooling on ice for 30 s. (A) Photograph of the 96-well plate after a 30-min incubation at 65°C, taken with a mobile phone. Wells with a yellow color indicate successful RT-LAMP amplification of a fragment of the SARS-CoV-2 N gene (using the N-A primer set). (B) Quantification of the red-to-yellow color change in all wells using spectrophotometric OD measurements. The color value at the given time points is quantified as the difference between the wavelengths of the two absorbance maxima of phenol red: ΔOD = OD434 nm – OD560 nm. Yellow (positive) samples yield a ΔOD of about 0.3 to 0.4. Each line represents one sample. For each sample, the line color indicates the CT (cycle threshold) value obtained from RT-qPCR data (using the E-Sarbeco primers) (15). (C) Scatter plot of ΔOD values at the 30-min time point from (B) compared to CT values from RT-qPCR. Each dot is one sample (well)."}