PMC:7068162 / 2086-3275 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"30","span":{"begin":83,"end":84},"obj":"Gene"},{"id":"31","span":{"begin":741,"end":746},"obj":"Chemical"}],"attributes":[{"id":"A30","pred":"tao:has_database_id","subj":"30","obj":"Gene:43740570"},{"id":"A31","pred":"tao:has_database_id","subj":"31","obj":"MESH:D014867"}],"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":"A custom-made primer/probe set based on a previously published assay targeting the E gene [4] was optimised for the use on the automated system. Primer and probes were ordered from IDT DNA Technologies (Coralville, United States (US)). Both primers were modified with 2’-O-methyl bases in their penultimate base to prevent formation of primer dimers. The ZEN double-quenched probe (IDT) was used in order to lower background fluorescence. The master mix (Mmx) cassette (for 96 tests) is prepared by combining 84 µL forward primer (400 nM, 5´-ACAGGTACGTTAATAGTTAATAGCmGT-3´), 84 µL reverse primer (400 nM, 5´-ATATTGCAGCAGTACGCACAmCA-3´) and 10.5 µL probe (50 nM, 5´-Fam-ACACTAGCC/ZEN/ATCCTTACTGCGCTTCG-Iowa Black FQ-3’)* together with 182 µL water and 5,640 µl Mmx2 mixture. After mixing, the 6 mL are transferred to the reagent cassette. The Mmx cassette is delivered with a full-process control: it is preloaded with an internal control (IC) RNA together with primers and probe of the IC detection assay by default [6]. Instrument settings in the cobas mni Utility Channel software (Roche, Los Gatos, US) and the temperature profile used for the RT-PCR reaction are summarised in Table 1."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T1","span":{"begin":85,"end":89},"obj":"Body_part"},{"id":"T2","span":{"begin":185,"end":188},"obj":"Body_part"},{"id":"T3","span":{"begin":943,"end":946},"obj":"Body_part"}],"attributes":[{"id":"A1","pred":"fma_id","subj":"T1","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A2","pred":"fma_id","subj":"T2","obj":"http://purl.org/sig/ont/fma/fma74412"},{"id":"A3","pred":"fma_id","subj":"T3","obj":"http://purl.org/sig/ont/fma/fma67095"}],"text":"A custom-made primer/probe set based on a previously published assay targeting the E gene [4] was optimised for the use on the automated system. Primer and probes were ordered from IDT DNA Technologies (Coralville, United States (US)). Both primers were modified with 2’-O-methyl bases in their penultimate base to prevent formation of primer dimers. The ZEN double-quenched probe (IDT) was used in order to lower background fluorescence. The master mix (Mmx) cassette (for 96 tests) is prepared by combining 84 µL forward primer (400 nM, 5´-ACAGGTACGTTAATAGTTAATAGCmGT-3´), 84 µL reverse primer (400 nM, 5´-ATATTGCAGCAGTACGCACAmCA-3´) and 10.5 µL probe (50 nM, 5´-Fam-ACACTAGCC/ZEN/ATCCTTACTGCGCTTCG-Iowa Black FQ-3’)* together with 182 µL water and 5,640 µl Mmx2 mixture. After mixing, the 6 mL are transferred to the reagent cassette. The Mmx cassette is delivered with a full-process control: it is preloaded with an internal control (IC) RNA together with primers and probe of the IC detection assay by default [6]. Instrument settings in the cobas mni Utility Channel software (Roche, Los Gatos, US) and the temperature profile used for the RT-PCR reaction are summarised in Table 1."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T20","span":{"begin":0,"end":1},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T21","span":{"begin":40,"end":41},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T22","span":{"begin":85,"end":89},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T23","span":{"begin":477,"end":482},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T24","span":{"begin":873,"end":874},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T25","span":{"begin":1021,"end":1031},"obj":"http://purl.obolibrary.org/obo/OBI_0000968"}],"text":"A custom-made primer/probe set based on a previously published assay targeting the E gene [4] was optimised for the use on the automated system. Primer and probes were ordered from IDT DNA Technologies (Coralville, United States (US)). Both primers were modified with 2’-O-methyl bases in their penultimate base to prevent formation of primer dimers. The ZEN double-quenched probe (IDT) was used in order to lower background fluorescence. The master mix (Mmx) cassette (for 96 tests) is prepared by combining 84 µL forward primer (400 nM, 5´-ACAGGTACGTTAATAGTTAATAGCmGT-3´), 84 µL reverse primer (400 nM, 5´-ATATTGCAGCAGTACGCACAmCA-3´) and 10.5 µL probe (50 nM, 5´-Fam-ACACTAGCC/ZEN/ATCCTTACTGCGCTTCG-Iowa Black FQ-3’)* together with 182 µL water and 5,640 µl Mmx2 mixture. After mixing, the 6 mL are transferred to the reagent cassette. The Mmx cassette is delivered with a full-process control: it is preloaded with an internal control (IC) RNA together with primers and probe of the IC detection assay by default [6]. Instrument settings in the cobas mni Utility Channel software (Roche, Los Gatos, US) and the temperature profile used for the RT-PCR reaction are summarised in Table 1."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T1","span":{"begin":21,"end":26},"obj":"Chemical"},{"id":"T2","span":{"begin":185,"end":188},"obj":"Chemical"},{"id":"T3","span":{"begin":273,"end":279},"obj":"Chemical"},{"id":"T5","span":{"begin":280,"end":285},"obj":"Chemical"},{"id":"T6","span":{"begin":307,"end":311},"obj":"Chemical"},{"id":"T7","span":{"begin":375,"end":380},"obj":"Chemical"},{"id":"T8","span":{"begin":648,"end":653},"obj":"Chemical"},{"id":"T9","span":{"begin":741,"end":746},"obj":"Chemical"},{"id":"T10","span":{"begin":765,"end":772},"obj":"Chemical"},{"id":"T11","span":{"begin":820,"end":827},"obj":"Chemical"},{"id":"T12","span":{"begin":973,"end":978},"obj":"Chemical"}],"attributes":[{"id":"A1","pred":"chebi_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/CHEBI_50406"},{"id":"A2","pred":"chebi_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"},{"id":"A3","pred":"chebi_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/CHEBI_32875"},{"id":"A4","pred":"chebi_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/CHEBI_29309"},{"id":"A5","pred":"chebi_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/CHEBI_22695"},{"id":"A6","pred":"chebi_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/CHEBI_22695"},{"id":"A7","pred":"chebi_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/CHEBI_50406"},{"id":"A8","pred":"chebi_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/CHEBI_50406"},{"id":"A9","pred":"chebi_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/CHEBI_15377"},{"id":"A10","pred":"chebi_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/CHEBI_60004"},{"id":"A11","pred":"chebi_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/CHEBI_33893"},{"id":"A12","pred":"chebi_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/CHEBI_50406"}],"text":"A custom-made primer/probe set based on a previously published assay targeting the E gene [4] was optimised for the use on the automated system. Primer and probes were ordered from IDT DNA Technologies (Coralville, United States (US)). Both primers were modified with 2’-O-methyl bases in their penultimate base to prevent formation of primer dimers. The ZEN double-quenched probe (IDT) was used in order to lower background fluorescence. The master mix (Mmx) cassette (for 96 tests) is prepared by combining 84 µL forward primer (400 nM, 5´-ACAGGTACGTTAATAGTTAATAGCmGT-3´), 84 µL reverse primer (400 nM, 5´-ATATTGCAGCAGTACGCACAmCA-3´) and 10.5 µL probe (50 nM, 5´-Fam-ACACTAGCC/ZEN/ATCCTTACTGCGCTTCG-Iowa Black FQ-3’)* together with 182 µL water and 5,640 µl Mmx2 mixture. After mixing, the 6 mL are transferred to the reagent cassette. The Mmx cassette is delivered with a full-process control: it is preloaded with an internal control (IC) RNA together with primers and probe of the IC detection assay by default [6]. Instrument settings in the cobas mni Utility Channel software (Roche, Los Gatos, US) and the temperature profile used for the RT-PCR reaction are summarised in Table 1."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T1","span":{"begin":323,"end":332},"obj":"http://purl.obolibrary.org/obo/GO_0009058"}],"text":"A custom-made primer/probe set based on a previously published assay targeting the E gene [4] was optimised for the use on the automated system. Primer and probes were ordered from IDT DNA Technologies (Coralville, United States (US)). Both primers were modified with 2’-O-methyl bases in their penultimate base to prevent formation of primer dimers. The ZEN double-quenched probe (IDT) was used in order to lower background fluorescence. The master mix (Mmx) cassette (for 96 tests) is prepared by combining 84 µL forward primer (400 nM, 5´-ACAGGTACGTTAATAGTTAATAGCmGT-3´), 84 µL reverse primer (400 nM, 5´-ATATTGCAGCAGTACGCACAmCA-3´) and 10.5 µL probe (50 nM, 5´-Fam-ACACTAGCC/ZEN/ATCCTTACTGCGCTTCG-Iowa Black FQ-3’)* together with 182 µL water and 5,640 µl Mmx2 mixture. After mixing, the 6 mL are transferred to the reagent cassette. The Mmx cassette is delivered with a full-process control: it is preloaded with an internal control (IC) RNA together with primers and probe of the IC detection assay by default [6]. Instrument settings in the cobas mni Utility Channel software (Roche, Los Gatos, US) and the temperature profile used for the RT-PCR reaction are summarised in Table 1."}

{"project":"LitCovid-sentences","denotations":[{"id":"T15","span":{"begin":0,"end":144},"obj":"Sentence"},{"id":"T16","span":{"begin":145,"end":235},"obj":"Sentence"},{"id":"T17","span":{"begin":236,"end":350},"obj":"Sentence"},{"id":"T18","span":{"begin":351,"end":438},"obj":"Sentence"},{"id":"T19","span":{"begin":439,"end":773},"obj":"Sentence"},{"id":"T20","span":{"begin":774,"end":837},"obj":"Sentence"},{"id":"T21","span":{"begin":838,"end":1020},"obj":"Sentence"},{"id":"T22","span":{"begin":1021,"end":1189},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"A custom-made primer/probe set based on a previously published assay targeting the E gene [4] was optimised for the use on the automated system. Primer and probes were ordered from IDT DNA Technologies (Coralville, United States (US)). Both primers were modified with 2’-O-methyl bases in their penultimate base to prevent formation of primer dimers. The ZEN double-quenched probe (IDT) was used in order to lower background fluorescence. The master mix (Mmx) cassette (for 96 tests) is prepared by combining 84 µL forward primer (400 nM, 5´-ACAGGTACGTTAATAGTTAATAGCmGT-3´), 84 µL reverse primer (400 nM, 5´-ATATTGCAGCAGTACGCACAmCA-3´) and 10.5 µL probe (50 nM, 5´-Fam-ACACTAGCC/ZEN/ATCCTTACTGCGCTTCG-Iowa Black FQ-3’)* together with 182 µL water and 5,640 µl Mmx2 mixture. After mixing, the 6 mL are transferred to the reagent cassette. The Mmx cassette is delivered with a full-process control: it is preloaded with an internal control (IC) RNA together with primers and probe of the IC detection assay by default [6]. Instrument settings in the cobas mni Utility Channel software (Roche, Los Gatos, US) and the temperature profile used for the RT-PCR reaction are summarised in Table 1."}

{"project":"2_test","denotations":[{"id":"32156329-31992387-29322903","span":{"begin":91,"end":92},"obj":"31992387"},{"id":"32156329-29322525-29322904","span":{"begin":1017,"end":1018},"obj":"29322525"}],"text":"A custom-made primer/probe set based on a previously published assay targeting the E gene [4] was optimised for the use on the automated system. Primer and probes were ordered from IDT DNA Technologies (Coralville, United States (US)). Both primers were modified with 2’-O-methyl bases in their penultimate base to prevent formation of primer dimers. The ZEN double-quenched probe (IDT) was used in order to lower background fluorescence. The master mix (Mmx) cassette (for 96 tests) is prepared by combining 84 µL forward primer (400 nM, 5´-ACAGGTACGTTAATAGTTAATAGCmGT-3´), 84 µL reverse primer (400 nM, 5´-ATATTGCAGCAGTACGCACAmCA-3´) and 10.5 µL probe (50 nM, 5´-Fam-ACACTAGCC/ZEN/ATCCTTACTGCGCTTCG-Iowa Black FQ-3’)* together with 182 µL water and 5,640 µl Mmx2 mixture. After mixing, the 6 mL are transferred to the reagent cassette. The Mmx cassette is delivered with a full-process control: it is preloaded with an internal control (IC) RNA together with primers and probe of the IC detection assay by default [6]. Instrument settings in the cobas mni Utility Channel software (Roche, Los Gatos, US) and the temperature profile used for the RT-PCR reaction are summarised in Table 1."}

{"project":"MyTest","denotations":[{"id":"32156329-31992387-29322903","span":{"begin":91,"end":92},"obj":"31992387"},{"id":"32156329-29322525-29322904","span":{"begin":1017,"end":1018},"obj":"29322525"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"A custom-made primer/probe set based on a previously published assay targeting the E gene [4] was optimised for the use on the automated system. Primer and probes were ordered from IDT DNA Technologies (Coralville, United States (US)). Both primers were modified with 2’-O-methyl bases in their penultimate base to prevent formation of primer dimers. The ZEN double-quenched probe (IDT) was used in order to lower background fluorescence. The master mix (Mmx) cassette (for 96 tests) is prepared by combining 84 µL forward primer (400 nM, 5´-ACAGGTACGTTAATAGTTAATAGCmGT-3´), 84 µL reverse primer (400 nM, 5´-ATATTGCAGCAGTACGCACAmCA-3´) and 10.5 µL probe (50 nM, 5´-Fam-ACACTAGCC/ZEN/ATCCTTACTGCGCTTCG-Iowa Black FQ-3’)* together with 182 µL water and 5,640 µl Mmx2 mixture. After mixing, the 6 mL are transferred to the reagent cassette. The Mmx cassette is delivered with a full-process control: it is preloaded with an internal control (IC) RNA together with primers and probe of the IC detection assay by default [6]. Instrument settings in the cobas mni Utility Channel software (Roche, Los Gatos, US) and the temperature profile used for the RT-PCR reaction are summarised in Table 1."}