PMC:6988269 / 6534-7844 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T16","span":{"begin":132,"end":136},"obj":"Body_part"},{"id":"T17","span":{"begin":574,"end":578},"obj":"Body_part"},{"id":"T18","span":{"begin":782,"end":786},"obj":"Body_part"},{"id":"T19","span":{"begin":1006,"end":1010},"obj":"Body_part"}],"attributes":[{"id":"A16","pred":"fma_id","subj":"T16","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A17","pred":"fma_id","subj":"T17","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A18","pred":"fma_id","subj":"T18","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A19","pred":"fma_id","subj":"T19","obj":"http://purl.org/sig/ont/fma/fma284995"}],"text":"Table 1 Primers and probes, real-time RT-PCR for 2019 novel coronavirus\nAssay/use Oligonucleotide Sequencea Concentrationb\nRdRP gene RdRp_SARSr-F GTGARATGGTCATGTGTGGCGG Use 600 nM per reaction\nRdRp_SARSr-P2 FAM-CAGGTGGAACCTCATCAGGAGATGC-BBQ Specific for 2019-nCoV, will not detect SARS-CoV.Use 100 nM per reaction and mix with P1\nRdRP_SARSr-P1 FAM-CCAGGTGGWACRTCATCMGGTGATGC-BBQ Pan Sarbeco-Probe will detect 2019-nCoV, SARS-CoV and bat-SARS-related CoVs.Use 100 nM per reaction and mix with P2\nRdRp_SARSr-R CARATGTTAAASACACTATTAGCATA Use 800 nM per reaction\nE gene E_Sarbeco_F ACAGGTACGTTAATAGTTAATAGCGT Use 400 nm per reaction\nE_Sarbeco_P1 FAM-ACACTAGCCATCCTTACTGCGCTTCG-BBQ Use 200 nm per reaction\nE_Sarbeco_R ATATTGCAGCAGTACGCACACA Use 400 nm per reaction\nN gene N_Sarbeco_F CACATTGGCACCCGCAATC Use 600 nm per reaction\nN_Sarbeco_P FAM-ACTTCCTCAAGGAACAACATTGCCA-BBQ Use 200 nm per reaction\nN_Sarbeco_R GAGGAACGAGAAGAGGCTTG Use 800 nm per reaction\na W is A/T; R is G/A; M is A/C; S is G/C. FAM: 6-carboxyfluorescein; BBQ: blackberry quencher.\nb Optimised concentrations are given in nanomol per litre (nM) based on the final reaction mix, e.g. 1.5 µL of a 10 µM primer stock solution per 25 µL total reaction volume yields a final concentration of 600 nM as indicated in the table."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T14","span":{"begin":290,"end":294},"obj":"Disease"},{"id":"T15","span":{"begin":431,"end":439},"obj":"Disease"},{"id":"T16","span":{"begin":431,"end":435},"obj":"Disease"},{"id":"T17","span":{"begin":448,"end":452},"obj":"Disease"}],"attributes":[{"id":"A14","pred":"mondo_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A15","pred":"mondo_id","subj":"T15","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A16","pred":"mondo_id","subj":"T16","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A17","pred":"mondo_id","subj":"T17","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Table 1 Primers and probes, real-time RT-PCR for 2019 novel coronavirus\nAssay/use Oligonucleotide Sequencea Concentrationb\nRdRP gene RdRp_SARSr-F GTGARATGGTCATGTGTGGCGG Use 600 nM per reaction\nRdRp_SARSr-P2 FAM-CAGGTGGAACCTCATCAGGAGATGC-BBQ Specific for 2019-nCoV, will not detect SARS-CoV.Use 100 nM per reaction and mix with P1\nRdRP_SARSr-P1 FAM-CCAGGTGGWACRTCATCMGGTGATGC-BBQ Pan Sarbeco-Probe will detect 2019-nCoV, SARS-CoV and bat-SARS-related CoVs.Use 100 nM per reaction and mix with P2\nRdRp_SARSr-R CARATGTTAAASACACTATTAGCATA Use 800 nM per reaction\nE gene E_Sarbeco_F ACAGGTACGTTAATAGTTAATAGCGT Use 400 nm per reaction\nE_Sarbeco_P1 FAM-ACACTAGCCATCCTTACTGCGCTTCG-BBQ Use 200 nm per reaction\nE_Sarbeco_R ATATTGCAGCAGTACGCACACA Use 400 nm per reaction\nN gene N_Sarbeco_F CACATTGGCACCCGCAATC Use 600 nm per reaction\nN_Sarbeco_P FAM-ACTTCCTCAAGGAACAACATTGCCA-BBQ Use 200 nm per reaction\nN_Sarbeco_R GAGGAACGAGAAGAGGCTTG Use 800 nm per reaction\na W is A/T; R is G/A; M is A/C; S is G/C. FAM: 6-carboxyfluorescein; BBQ: blackberry quencher.\nb Optimised concentrations are given in nanomol per litre (nM) based on the final reaction mix, e.g. 1.5 µL of a 10 µM primer stock solution per 25 µL total reaction volume yields a final concentration of 600 nM as indicated in the table."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T54","span":{"begin":132,"end":136},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T55","span":{"begin":211,"end":213},"obj":"http://purl.obolibrary.org/obo/CLO_0008307"},{"id":"T56","span":{"begin":336,"end":338},"obj":"http://purl.obolibrary.org/obo/CLO_0008285"},{"id":"T57","span":{"begin":350,"end":352},"obj":"http://purl.obolibrary.org/obo/CLO_0008285"},{"id":"T58","span":{"begin":390,"end":393},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9596"},{"id":"T59","span":{"begin":444,"end":447},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T60","span":{"begin":503,"end":505},"obj":"http://purl.obolibrary.org/obo/CLO_0008307"},{"id":"T61","span":{"begin":574,"end":578},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T62","span":{"begin":782,"end":786},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T63","span":{"begin":977,"end":978},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T64","span":{"begin":984,"end":985},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T65","span":{"begin":996,"end":997},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T66","span":{"begin":1004,"end":1005},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T67","span":{"begin":1072,"end":1073},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T68","span":{"begin":1183,"end":1187},"obj":"http://purl.obolibrary.org/obo/CLO_0001550"},{"id":"T69","span":{"begin":1252,"end":1253},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"Table 1 Primers and probes, real-time RT-PCR for 2019 novel coronavirus\nAssay/use Oligonucleotide Sequencea Concentrationb\nRdRP gene RdRp_SARSr-F GTGARATGGTCATGTGTGGCGG Use 600 nM per reaction\nRdRp_SARSr-P2 FAM-CAGGTGGAACCTCATCAGGAGATGC-BBQ Specific for 2019-nCoV, will not detect SARS-CoV.Use 100 nM per reaction and mix with P1\nRdRP_SARSr-P1 FAM-CCAGGTGGWACRTCATCMGGTGATGC-BBQ Pan Sarbeco-Probe will detect 2019-nCoV, SARS-CoV and bat-SARS-related CoVs.Use 100 nM per reaction and mix with P2\nRdRp_SARSr-R CARATGTTAAASACACTATTAGCATA Use 800 nM per reaction\nE gene E_Sarbeco_F ACAGGTACGTTAATAGTTAATAGCGT Use 400 nm per reaction\nE_Sarbeco_P1 FAM-ACACTAGCCATCCTTACTGCGCTTCG-BBQ Use 200 nm per reaction\nE_Sarbeco_R ATATTGCAGCAGTACGCACACA Use 400 nm per reaction\nN gene N_Sarbeco_F CACATTGGCACCCGCAATC Use 600 nm per reaction\nN_Sarbeco_P FAM-ACTTCCTCAAGGAACAACATTGCCA-BBQ Use 200 nm per reaction\nN_Sarbeco_R GAGGAACGAGAAGAGGCTTG Use 800 nm per reaction\na W is A/T; R is G/A; M is A/C; S is G/C. FAM: 6-carboxyfluorescein; BBQ: blackberry quencher.\nb Optimised concentrations are given in nanomol per litre (nM) based on the final reaction mix, e.g. 1.5 µL of a 10 µM primer stock solution per 25 µL total reaction volume yields a final concentration of 600 nM as indicated in the table."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T19","span":{"begin":84,"end":99},"obj":"Chemical"},{"id":"T20","span":{"begin":211,"end":213},"obj":"Chemical"},{"id":"T21","span":{"begin":336,"end":338},"obj":"Chemical"},{"id":"T22","span":{"begin":350,"end":352},"obj":"Chemical"},{"id":"T23","span":{"begin":503,"end":505},"obj":"Chemical"},{"id":"T24","span":{"begin":1024,"end":1044},"obj":"Chemical"},{"id":"T25","span":{"begin":1204,"end":1212},"obj":"Chemical"}],"attributes":[{"id":"A19","pred":"chebi_id","subj":"T19","obj":"http://purl.obolibrary.org/obo/CHEBI_7754"},{"id":"A20","pred":"chebi_id","subj":"T20","obj":"http://purl.obolibrary.org/obo/CHEBI_33472"},{"id":"A21","pred":"chebi_id","subj":"T21","obj":"http://purl.obolibrary.org/obo/CHEBI_60949"},{"id":"A22","pred":"chebi_id","subj":"T22","obj":"http://purl.obolibrary.org/obo/CHEBI_60949"},{"id":"A23","pred":"chebi_id","subj":"T23","obj":"http://purl.obolibrary.org/obo/CHEBI_33472"},{"id":"A24","pred":"chebi_id","subj":"T24","obj":"http://purl.obolibrary.org/obo/CHEBI_39073"},{"id":"A25","pred":"chebi_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/CHEBI_75958"}],"text":"Table 1 Primers and probes, real-time RT-PCR for 2019 novel coronavirus\nAssay/use Oligonucleotide Sequencea Concentrationb\nRdRP gene RdRp_SARSr-F GTGARATGGTCATGTGTGGCGG Use 600 nM per reaction\nRdRp_SARSr-P2 FAM-CAGGTGGAACCTCATCAGGAGATGC-BBQ Specific for 2019-nCoV, will not detect SARS-CoV.Use 100 nM per reaction and mix with P1\nRdRP_SARSr-P1 FAM-CCAGGTGGWACRTCATCMGGTGATGC-BBQ Pan Sarbeco-Probe will detect 2019-nCoV, SARS-CoV and bat-SARS-related CoVs.Use 100 nM per reaction and mix with P2\nRdRp_SARSr-R CARATGTTAAASACACTATTAGCATA Use 800 nM per reaction\nE gene E_Sarbeco_F ACAGGTACGTTAATAGTTAATAGCGT Use 400 nm per reaction\nE_Sarbeco_P1 FAM-ACACTAGCCATCCTTACTGCGCTTCG-BBQ Use 200 nm per reaction\nE_Sarbeco_R ATATTGCAGCAGTACGCACACA Use 400 nm per reaction\nN gene N_Sarbeco_F CACATTGGCACCCGCAATC Use 600 nm per reaction\nN_Sarbeco_P FAM-ACTTCCTCAAGGAACAACATTGCCA-BBQ Use 200 nm per reaction\nN_Sarbeco_R GAGGAACGAGAAGAGGCTTG Use 800 nm per reaction\na W is A/T; R is G/A; M is A/C; S is G/C. FAM: 6-carboxyfluorescein; BBQ: blackberry quencher.\nb Optimised concentrations are given in nanomol per litre (nM) based on the final reaction mix, e.g. 1.5 µL of a 10 µM primer stock solution per 25 µL total reaction volume yields a final concentration of 600 nM as indicated in the table."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T10","span":{"begin":127,"end":131},"obj":"http://purl.obolibrary.org/obo/GO_0003968"}],"text":"Table 1 Primers and probes, real-time RT-PCR for 2019 novel coronavirus\nAssay/use Oligonucleotide Sequencea Concentrationb\nRdRP gene RdRp_SARSr-F GTGARATGGTCATGTGTGGCGG Use 600 nM per reaction\nRdRp_SARSr-P2 FAM-CAGGTGGAACCTCATCAGGAGATGC-BBQ Specific for 2019-nCoV, will not detect SARS-CoV.Use 100 nM per reaction and mix with P1\nRdRP_SARSr-P1 FAM-CCAGGTGGWACRTCATCMGGTGATGC-BBQ Pan Sarbeco-Probe will detect 2019-nCoV, SARS-CoV and bat-SARS-related CoVs.Use 100 nM per reaction and mix with P2\nRdRp_SARSr-R CARATGTTAAASACACTATTAGCATA Use 800 nM per reaction\nE gene E_Sarbeco_F ACAGGTACGTTAATAGTTAATAGCGT Use 400 nm per reaction\nE_Sarbeco_P1 FAM-ACACTAGCCATCCTTACTGCGCTTCG-BBQ Use 200 nm per reaction\nE_Sarbeco_R ATATTGCAGCAGTACGCACACA Use 400 nm per reaction\nN gene N_Sarbeco_F CACATTGGCACCCGCAATC Use 600 nm per reaction\nN_Sarbeco_P FAM-ACTTCCTCAAGGAACAACATTGCCA-BBQ Use 200 nm per reaction\nN_Sarbeco_R GAGGAACGAGAAGAGGCTTG Use 800 nm per reaction\na W is A/T; R is G/A; M is A/C; S is G/C. FAM: 6-carboxyfluorescein; BBQ: blackberry quencher.\nb Optimised concentrations are given in nanomol per litre (nM) based on the final reaction mix, e.g. 1.5 µL of a 10 µM primer stock solution per 25 µL total reaction volume yields a final concentration of 600 nM as indicated in the table."}

{"project":"LitCovid-sentences","denotations":[{"id":"T47","span":{"begin":0,"end":72},"obj":"Sentence"},{"id":"T48","span":{"begin":73,"end":126},"obj":"Sentence"},{"id":"T49","span":{"begin":127,"end":199},"obj":"Sentence"},{"id":"T50","span":{"begin":200,"end":338},"obj":"Sentence"},{"id":"T51","span":{"begin":339,"end":505},"obj":"Sentence"},{"id":"T52","span":{"begin":506,"end":571},"obj":"Sentence"},{"id":"T53","span":{"begin":572,"end":644},"obj":"Sentence"},{"id":"T54","span":{"begin":645,"end":718},"obj":"Sentence"},{"id":"T55","span":{"begin":719,"end":779},"obj":"Sentence"},{"id":"T56","span":{"begin":780,"end":845},"obj":"Sentence"},{"id":"T57","span":{"begin":846,"end":917},"obj":"Sentence"},{"id":"T58","span":{"begin":918,"end":976},"obj":"Sentence"},{"id":"T59","span":{"begin":977,"end":1018},"obj":"Sentence"},{"id":"T60","span":{"begin":1019,"end":1023},"obj":"Sentence"},{"id":"T61","span":{"begin":1024,"end":1071},"obj":"Sentence"},{"id":"T62","span":{"begin":1072,"end":1310},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Table 1 Primers and probes, real-time RT-PCR for 2019 novel coronavirus\nAssay/use Oligonucleotide Sequencea Concentrationb\nRdRP gene RdRp_SARSr-F GTGARATGGTCATGTGTGGCGG Use 600 nM per reaction\nRdRp_SARSr-P2 FAM-CAGGTGGAACCTCATCAGGAGATGC-BBQ Specific for 2019-nCoV, will not detect SARS-CoV.Use 100 nM per reaction and mix with P1\nRdRP_SARSr-P1 FAM-CCAGGTGGWACRTCATCMGGTGATGC-BBQ Pan Sarbeco-Probe will detect 2019-nCoV, SARS-CoV and bat-SARS-related CoVs.Use 100 nM per reaction and mix with P2\nRdRp_SARSr-R CARATGTTAAASACACTATTAGCATA Use 800 nM per reaction\nE gene E_Sarbeco_F ACAGGTACGTTAATAGTTAATAGCGT Use 400 nm per reaction\nE_Sarbeco_P1 FAM-ACACTAGCCATCCTTACTGCGCTTCG-BBQ Use 200 nm per reaction\nE_Sarbeco_R ATATTGCAGCAGTACGCACACA Use 400 nm per reaction\nN gene N_Sarbeco_F CACATTGGCACCCGCAATC Use 600 nm per reaction\nN_Sarbeco_P FAM-ACTTCCTCAAGGAACAACATTGCCA-BBQ Use 200 nm per reaction\nN_Sarbeco_R GAGGAACGAGAAGAGGCTTG Use 800 nm per reaction\na W is A/T; R is G/A; M is A/C; S is G/C. FAM: 6-carboxyfluorescein; BBQ: blackberry quencher.\nb Optimised concentrations are given in nanomol per litre (nM) based on the final reaction mix, e.g. 1.5 µL of a 10 µM primer stock solution per 25 µL total reaction volume yields a final concentration of 600 nM as indicated in the table."}

{"project":"LitCovid-PubTator","denotations":[{"id":"125","span":{"begin":494,"end":497},"obj":"Gene"},{"id":"126","span":{"begin":327,"end":330},"obj":"Gene"},{"id":"127","span":{"begin":263,"end":272},"obj":"Species"},{"id":"128","span":{"begin":290,"end":298},"obj":"Species"},{"id":"129","span":{"begin":420,"end":429},"obj":"Species"},{"id":"130","span":{"begin":431,"end":439},"obj":"Species"},{"id":"131","span":{"begin":448,"end":465},"obj":"Species"},{"id":"133","span":{"begin":50,"end":72},"obj":"Species"},{"id":"135","span":{"begin":1024,"end":1044},"obj":"Chemical"},{"id":"137","span":{"begin":1163,"end":1166},"obj":"Gene"}],"attributes":[{"id":"A125","pred":"tao:has_database_id","subj":"125","obj":"Gene:83881"},{"id":"A126","pred":"tao:has_database_id","subj":"126","obj":"Gene:83881"},{"id":"A127","pred":"tao:has_database_id","subj":"127","obj":"Tax:2697049"},{"id":"A128","pred":"tao:has_database_id","subj":"128","obj":"Tax:694009"},{"id":"A129","pred":"tao:has_database_id","subj":"129","obj":"Tax:2697049"},{"id":"A130","pred":"tao:has_database_id","subj":"130","obj":"Tax:694009"},{"id":"A131","pred":"tao:has_database_id","subj":"131","obj":"Tax:694009"},{"id":"A133","pred":"tao:has_database_id","subj":"133","obj":"Tax:2697049"},{"id":"A135","pred":"tao:has_database_id","subj":"135","obj":"MESH:C024098"},{"id":"A137","pred":"tao:has_database_id","subj":"137","obj":"Gene:83881"}],"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":"Table 1 Primers and probes, real-time RT-PCR for 2019 novel coronavirus\nAssay/use Oligonucleotide Sequencea Concentrationb\nRdRP gene RdRp_SARSr-F GTGARATGGTCATGTGTGGCGG Use 600 nM per reaction\nRdRp_SARSr-P2 FAM-CAGGTGGAACCTCATCAGGAGATGC-BBQ Specific for 2019-nCoV, will not detect SARS-CoV.Use 100 nM per reaction and mix with P1\nRdRP_SARSr-P1 FAM-CCAGGTGGWACRTCATCMGGTGATGC-BBQ Pan Sarbeco-Probe will detect 2019-nCoV, SARS-CoV and bat-SARS-related CoVs.Use 100 nM per reaction and mix with P2\nRdRp_SARSr-R CARATGTTAAASACACTATTAGCATA Use 800 nM per reaction\nE gene E_Sarbeco_F ACAGGTACGTTAATAGTTAATAGCGT Use 400 nm per reaction\nE_Sarbeco_P1 FAM-ACACTAGCCATCCTTACTGCGCTTCG-BBQ Use 200 nm per reaction\nE_Sarbeco_R ATATTGCAGCAGTACGCACACA Use 400 nm per reaction\nN gene N_Sarbeco_F CACATTGGCACCCGCAATC Use 600 nm per reaction\nN_Sarbeco_P FAM-ACTTCCTCAAGGAACAACATTGCCA-BBQ Use 200 nm per reaction\nN_Sarbeco_R GAGGAACGAGAAGAGGCTTG Use 800 nm per reaction\na W is A/T; R is G/A; M is A/C; S is G/C. FAM: 6-carboxyfluorescein; BBQ: blackberry quencher.\nb Optimised concentrations are given in nanomol per litre (nM) based on the final reaction mix, e.g. 1.5 µL of a 10 µM primer stock solution per 25 µL total reaction volume yields a final concentration of 600 nM as indicated in the table."}