PMC:7258756 / 7744-8766 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"145","span":{"begin":918,"end":921},"obj":"Gene"},{"id":"146","span":{"begin":881,"end":884},"obj":"Gene"},{"id":"147","span":{"begin":7,"end":17},"obj":"Species"},{"id":"148","span":{"begin":180,"end":190},"obj":"Species"},{"id":"149","span":{"begin":1011,"end":1021},"obj":"Species"}],"attributes":[{"id":"A145","pred":"tao:has_database_id","subj":"145","obj":"Gene:1178"},{"id":"A146","pred":"tao:has_database_id","subj":"146","obj":"Gene:1178"},{"id":"A147","pred":"tao:has_database_id","subj":"147","obj":"Tax:2697049"},{"id":"A148","pred":"tao:has_database_id","subj":"148","obj":"Tax:2697049"},{"id":"A149","pred":"tao:has_database_id","subj":"149","obj":"Tax:2697049"}],"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":"NGS of SARS-CoV-2 from India - Phylogenetic analysis and molecular characterization: The total RNA of three positive TS specimens from Kerala, was extracted from 250-300 μl of the SARS-CoV-2 real-time RT-PCR positive samples. QIAamp Viral RNA extraction kit (QIAGEN, Hilden, Germany) was used according to the manufacturer's instructions. The extracted RNA was further quantified using a Qubit RNA High-Sensitivity kit (Invitrogen, USA). RNA libraries were prepared as per the earlier-defined protocol and quantified using KAPA Library Quantification Kit (Kapa Biosystems, Roche Diagnostics Corporation, USA) as per the manufacturer's protocol. Further, individual libraries were neutralized and loaded on the Miniseq platform (Illumina, USA). The detailed protocols for the steps undertaken have been published earlier1516. The data generated from the machine were analyzed using CLC genomics workbench version 11.0 (CLC, QIAGEN, Germany). Reference-based mapping was performed to retrieve the sequence of the SARS-CoV-2."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T33","span":{"begin":95,"end":98},"obj":"Body_part"},{"id":"T34","span":{"begin":239,"end":242},"obj":"Body_part"},{"id":"T35","span":{"begin":353,"end":356},"obj":"Body_part"},{"id":"T36","span":{"begin":394,"end":397},"obj":"Body_part"},{"id":"T37","span":{"begin":438,"end":441},"obj":"Body_part"}],"attributes":[{"id":"A33","pred":"fma_id","subj":"T33","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A34","pred":"fma_id","subj":"T34","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A35","pred":"fma_id","subj":"T35","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A36","pred":"fma_id","subj":"T36","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A37","pred":"fma_id","subj":"T37","obj":"http://purl.org/sig/ont/fma/fma67095"}],"text":"NGS of SARS-CoV-2 from India - Phylogenetic analysis and molecular characterization: The total RNA of three positive TS specimens from Kerala, was extracted from 250-300 μl of the SARS-CoV-2 real-time RT-PCR positive samples. QIAamp Viral RNA extraction kit (QIAGEN, Hilden, Germany) was used according to the manufacturer's instructions. The extracted RNA was further quantified using a Qubit RNA High-Sensitivity kit (Invitrogen, USA). RNA libraries were prepared as per the earlier-defined protocol and quantified using KAPA Library Quantification Kit (Kapa Biosystems, Roche Diagnostics Corporation, USA) as per the manufacturer's protocol. Further, individual libraries were neutralized and loaded on the Miniseq platform (Illumina, USA). The detailed protocols for the steps undertaken have been published earlier1516. The data generated from the machine were analyzed using CLC genomics workbench version 11.0 (CLC, QIAGEN, Germany). Reference-based mapping was performed to retrieve the sequence of the SARS-CoV-2."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T73","span":{"begin":7,"end":15},"obj":"Disease"},{"id":"T74","span":{"begin":7,"end":11},"obj":"Disease"},{"id":"T75","span":{"begin":117,"end":119},"obj":"Disease"},{"id":"T77","span":{"begin":180,"end":188},"obj":"Disease"},{"id":"T78","span":{"begin":180,"end":184},"obj":"Disease"},{"id":"T79","span":{"begin":881,"end":884},"obj":"Disease"},{"id":"T80","span":{"begin":918,"end":921},"obj":"Disease"},{"id":"T81","span":{"begin":1011,"end":1019},"obj":"Disease"},{"id":"T82","span":{"begin":1011,"end":1015},"obj":"Disease"}],"attributes":[{"id":"A73","pred":"mondo_id","subj":"T73","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A74","pred":"mondo_id","subj":"T74","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A75","pred":"mondo_id","subj":"T75","obj":"http://purl.obolibrary.org/obo/MONDO_0010979"},{"id":"A76","pred":"mondo_id","subj":"T75","obj":"http://purl.obolibrary.org/obo/MONDO_0016455"},{"id":"A77","pred":"mondo_id","subj":"T77","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A78","pred":"mondo_id","subj":"T78","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A79","pred":"mondo_id","subj":"T79","obj":"http://purl.obolibrary.org/obo/MONDO_0004315"},{"id":"A80","pred":"mondo_id","subj":"T80","obj":"http://purl.obolibrary.org/obo/MONDO_0004315"},{"id":"A81","pred":"mondo_id","subj":"T81","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A82","pred":"mondo_id","subj":"T82","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"NGS of SARS-CoV-2 from India - Phylogenetic analysis and molecular characterization: The total RNA of three positive TS specimens from Kerala, was extracted from 250-300 μl of the SARS-CoV-2 real-time RT-PCR positive samples. QIAamp Viral RNA extraction kit (QIAGEN, Hilden, Germany) was used according to the manufacturer's instructions. The extracted RNA was further quantified using a Qubit RNA High-Sensitivity kit (Invitrogen, USA). RNA libraries were prepared as per the earlier-defined protocol and quantified using KAPA Library Quantification Kit (Kapa Biosystems, Roche Diagnostics Corporation, USA) as per the manufacturer's protocol. Further, individual libraries were neutralized and loaded on the Miniseq platform (Illumina, USA). The detailed protocols for the steps undertaken have been published earlier1516. The data generated from the machine were analyzed using CLC genomics workbench version 11.0 (CLC, QIAGEN, Germany). Reference-based mapping was performed to retrieve the sequence of the SARS-CoV-2."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T68","span":{"begin":386,"end":387},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T69","span":{"begin":881,"end":884},"obj":"http://purl.obolibrary.org/obo/CLO_0002494"},{"id":"T70","span":{"begin":918,"end":921},"obj":"http://purl.obolibrary.org/obo/CLO_0002494"}],"text":"NGS of SARS-CoV-2 from India - Phylogenetic analysis and molecular characterization: The total RNA of three positive TS specimens from Kerala, was extracted from 250-300 μl of the SARS-CoV-2 real-time RT-PCR positive samples. QIAamp Viral RNA extraction kit (QIAGEN, Hilden, Germany) was used according to the manufacturer's instructions. The extracted RNA was further quantified using a Qubit RNA High-Sensitivity kit (Invitrogen, USA). RNA libraries were prepared as per the earlier-defined protocol and quantified using KAPA Library Quantification Kit (Kapa Biosystems, Roche Diagnostics Corporation, USA) as per the manufacturer's protocol. Further, individual libraries were neutralized and loaded on the Miniseq platform (Illumina, USA). The detailed protocols for the steps undertaken have been published earlier1516. The data generated from the machine were analyzed using CLC genomics workbench version 11.0 (CLC, QIAGEN, Germany). Reference-based mapping was performed to retrieve the sequence of the SARS-CoV-2."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T17","span":{"begin":117,"end":119},"obj":"Chemical"}],"attributes":[{"id":"A17","pred":"chebi_id","subj":"T17","obj":"http://purl.obolibrary.org/obo/CHEBI_73664"}],"text":"NGS of SARS-CoV-2 from India - Phylogenetic analysis and molecular characterization: The total RNA of three positive TS specimens from Kerala, was extracted from 250-300 μl of the SARS-CoV-2 real-time RT-PCR positive samples. QIAamp Viral RNA extraction kit (QIAGEN, Hilden, Germany) was used according to the manufacturer's instructions. The extracted RNA was further quantified using a Qubit RNA High-Sensitivity kit (Invitrogen, USA). RNA libraries were prepared as per the earlier-defined protocol and quantified using KAPA Library Quantification Kit (Kapa Biosystems, Roche Diagnostics Corporation, USA) as per the manufacturer's protocol. Further, individual libraries were neutralized and loaded on the Miniseq platform (Illumina, USA). The detailed protocols for the steps undertaken have been published earlier1516. The data generated from the machine were analyzed using CLC genomics workbench version 11.0 (CLC, QIAGEN, Germany). Reference-based mapping was performed to retrieve the sequence of the SARS-CoV-2."}

{"project":"LitCovid-sentences","denotations":[{"id":"T61","span":{"begin":0,"end":84},"obj":"Sentence"},{"id":"T62","span":{"begin":85,"end":225},"obj":"Sentence"},{"id":"T63","span":{"begin":226,"end":338},"obj":"Sentence"},{"id":"T64","span":{"begin":339,"end":437},"obj":"Sentence"},{"id":"T65","span":{"begin":438,"end":644},"obj":"Sentence"},{"id":"T66","span":{"begin":645,"end":743},"obj":"Sentence"},{"id":"T67","span":{"begin":744,"end":824},"obj":"Sentence"},{"id":"T68","span":{"begin":825,"end":940},"obj":"Sentence"},{"id":"T69","span":{"begin":941,"end":1022},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"NGS of SARS-CoV-2 from India - Phylogenetic analysis and molecular characterization: The total RNA of three positive TS specimens from Kerala, was extracted from 250-300 μl of the SARS-CoV-2 real-time RT-PCR positive samples. QIAamp Viral RNA extraction kit (QIAGEN, Hilden, Germany) was used according to the manufacturer's instructions. The extracted RNA was further quantified using a Qubit RNA High-Sensitivity kit (Invitrogen, USA). RNA libraries were prepared as per the earlier-defined protocol and quantified using KAPA Library Quantification Kit (Kapa Biosystems, Roche Diagnostics Corporation, USA) as per the manufacturer's protocol. Further, individual libraries were neutralized and loaded on the Miniseq platform (Illumina, USA). The detailed protocols for the steps undertaken have been published earlier1516. The data generated from the machine were analyzed using CLC genomics workbench version 11.0 (CLC, QIAGEN, Germany). Reference-based mapping was performed to retrieve the sequence of the SARS-CoV-2."}

{"project":"2_test","denotations":[{"id":"32242873-29664366-47036564","span":{"begin":819,"end":821},"obj":"29664366"},{"id":"T53539","span":{"begin":819,"end":821},"obj":"29664366"}],"text":"NGS of SARS-CoV-2 from India - Phylogenetic analysis and molecular characterization: The total RNA of three positive TS specimens from Kerala, was extracted from 250-300 μl of the SARS-CoV-2 real-time RT-PCR positive samples. QIAamp Viral RNA extraction kit (QIAGEN, Hilden, Germany) was used according to the manufacturer's instructions. The extracted RNA was further quantified using a Qubit RNA High-Sensitivity kit (Invitrogen, USA). RNA libraries were prepared as per the earlier-defined protocol and quantified using KAPA Library Quantification Kit (Kapa Biosystems, Roche Diagnostics Corporation, USA) as per the manufacturer's protocol. Further, individual libraries were neutralized and loaded on the Miniseq platform (Illumina, USA). The detailed protocols for the steps undertaken have been published earlier1516. The data generated from the machine were analyzed using CLC genomics workbench version 11.0 (CLC, QIAGEN, Germany). Reference-based mapping was performed to retrieve the sequence of the SARS-CoV-2."}