PMC:7574920 / 20540-21711 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T102","span":{"begin":571,"end":574},"obj":"Body_part"},{"id":"T103","span":{"begin":1114,"end":1117},"obj":"Body_part"}],"attributes":[{"id":"A102","pred":"fma_id","subj":"T102","obj":"http://purl.org/sig/ont/fma/fma74412"},{"id":"A103","pred":"fma_id","subj":"T103","obj":"http://purl.org/sig/ont/fma/fma74412"}],"text":"Our results indicated that the colorimetric RT-LAMP assay enabled robust identification of positive samples after a 25- to 30-min incubation at 65°C. Validation of positive results, however, required confirmation that the RT-LAMP reaction led to the amplification of viral sequences. To analyze the sequences of many RT-LAMP reaction products, we established multiplexed sequencing of RT-LAMP products (LAMP-sequencing). LAMP-sequencing is based on Tn5 transposase tagmentation (17) and sample barcoding. Tagmentation enables fragmentation and direct adapter ligation of DNA samples for analysis by next-generation sequencing. We used a set of 96 barcoded adapters for tagmentation to barcode the RT-LAMP reaction products in each 96-well plate. After tagmentation, all barcoded fragments from each plate were pooled and size-selected by bead purification to remove excess adapters. A second set of barcoded primers, one per plate-pool, was then used to amplify the tagmented RT-LAMP fragments. Last, all amplified pools were combined for analysis using one next-generation sequencing run where the origin of each DNA fragment was specified by the two barcodes (Fig. 4A)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T202","span":{"begin":114,"end":115},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T203","span":{"begin":635,"end":636},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T204","span":{"begin":883,"end":884},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"Our results indicated that the colorimetric RT-LAMP assay enabled robust identification of positive samples after a 25- to 30-min incubation at 65°C. Validation of positive results, however, required confirmation that the RT-LAMP reaction led to the amplification of viral sequences. To analyze the sequences of many RT-LAMP reaction products, we established multiplexed sequencing of RT-LAMP products (LAMP-sequencing). LAMP-sequencing is based on Tn5 transposase tagmentation (17) and sample barcoding. Tagmentation enables fragmentation and direct adapter ligation of DNA samples for analysis by next-generation sequencing. We used a set of 96 barcoded adapters for tagmentation to barcode the RT-LAMP reaction products in each 96-well plate. After tagmentation, all barcoded fragments from each plate were pooled and size-selected by bead purification to remove excess adapters. A second set of barcoded primers, one per plate-pool, was then used to amplify the tagmented RT-LAMP fragments. Last, all amplified pools were combined for analysis using one next-generation sequencing run where the origin of each DNA fragment was specified by the two barcodes (Fig. 4A)."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T57","span":{"begin":571,"end":574},"obj":"Chemical"},{"id":"T58","span":{"begin":1114,"end":1117},"obj":"Chemical"}],"attributes":[{"id":"A57","pred":"chebi_id","subj":"T57","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"},{"id":"A58","pred":"chebi_id","subj":"T58","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"}],"text":"Our results indicated that the colorimetric RT-LAMP assay enabled robust identification of positive samples after a 25- to 30-min incubation at 65°C. Validation of positive results, however, required confirmation that the RT-LAMP reaction led to the amplification of viral sequences. To analyze the sequences of many RT-LAMP reaction products, we established multiplexed sequencing of RT-LAMP products (LAMP-sequencing). LAMP-sequencing is based on Tn5 transposase tagmentation (17) and sample barcoding. Tagmentation enables fragmentation and direct adapter ligation of DNA samples for analysis by next-generation sequencing. We used a set of 96 barcoded adapters for tagmentation to barcode the RT-LAMP reaction products in each 96-well plate. After tagmentation, all barcoded fragments from each plate were pooled and size-selected by bead purification to remove excess adapters. A second set of barcoded primers, one per plate-pool, was then used to amplify the tagmented RT-LAMP fragments. Last, all amplified pools were combined for analysis using one next-generation sequencing run where the origin of each DNA fragment was specified by the two barcodes (Fig. 4A)."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T122","span":{"begin":44,"end":46},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T123","span":{"begin":222,"end":224},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T124","span":{"begin":317,"end":319},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T125","span":{"begin":385,"end":387},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T126","span":{"begin":697,"end":699},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T127","span":{"begin":976,"end":978},"obj":"http://purl.obolibrary.org/obo/GO_0001171"}],"text":"Our results indicated that the colorimetric RT-LAMP assay enabled robust identification of positive samples after a 25- to 30-min incubation at 65°C. Validation of positive results, however, required confirmation that the RT-LAMP reaction led to the amplification of viral sequences. To analyze the sequences of many RT-LAMP reaction products, we established multiplexed sequencing of RT-LAMP products (LAMP-sequencing). LAMP-sequencing is based on Tn5 transposase tagmentation (17) and sample barcoding. Tagmentation enables fragmentation and direct adapter ligation of DNA samples for analysis by next-generation sequencing. We used a set of 96 barcoded adapters for tagmentation to barcode the RT-LAMP reaction products in each 96-well plate. After tagmentation, all barcoded fragments from each plate were pooled and size-selected by bead purification to remove excess adapters. A second set of barcoded primers, one per plate-pool, was then used to amplify the tagmented RT-LAMP fragments. Last, all amplified pools were combined for analysis using one next-generation sequencing run where the origin of each DNA fragment was specified by the two barcodes (Fig. 4A)."}

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T2","span":{"begin":449,"end":452},"obj":"GlycoEpitope"}],"attributes":[{"id":"A2","pred":"glyco_epitope_db_id","subj":"T2","obj":"http://www.glycoepitope.jp/epitopes/AN0083"}],"text":"Our results indicated that the colorimetric RT-LAMP assay enabled robust identification of positive samples after a 25- to 30-min incubation at 65°C. Validation of positive results, however, required confirmation that the RT-LAMP reaction led to the amplification of viral sequences. To analyze the sequences of many RT-LAMP reaction products, we established multiplexed sequencing of RT-LAMP products (LAMP-sequencing). LAMP-sequencing is based on Tn5 transposase tagmentation (17) and sample barcoding. Tagmentation enables fragmentation and direct adapter ligation of DNA samples for analysis by next-generation sequencing. We used a set of 96 barcoded adapters for tagmentation to barcode the RT-LAMP reaction products in each 96-well plate. After tagmentation, all barcoded fragments from each plate were pooled and size-selected by bead purification to remove excess adapters. A second set of barcoded primers, one per plate-pool, was then used to amplify the tagmented RT-LAMP fragments. Last, all amplified pools were combined for analysis using one next-generation sequencing run where the origin of each DNA fragment was specified by the two barcodes (Fig. 4A)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T139","span":{"begin":0,"end":149},"obj":"Sentence"},{"id":"T140","span":{"begin":150,"end":283},"obj":"Sentence"},{"id":"T141","span":{"begin":284,"end":420},"obj":"Sentence"},{"id":"T142","span":{"begin":421,"end":504},"obj":"Sentence"},{"id":"T143","span":{"begin":505,"end":626},"obj":"Sentence"},{"id":"T144","span":{"begin":627,"end":745},"obj":"Sentence"},{"id":"T145","span":{"begin":746,"end":882},"obj":"Sentence"},{"id":"T146","span":{"begin":883,"end":994},"obj":"Sentence"},{"id":"T147","span":{"begin":995,"end":1171},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Our results indicated that the colorimetric RT-LAMP assay enabled robust identification of positive samples after a 25- to 30-min incubation at 65°C. Validation of positive results, however, required confirmation that the RT-LAMP reaction led to the amplification of viral sequences. To analyze the sequences of many RT-LAMP reaction products, we established multiplexed sequencing of RT-LAMP products (LAMP-sequencing). LAMP-sequencing is based on Tn5 transposase tagmentation (17) and sample barcoding. Tagmentation enables fragmentation and direct adapter ligation of DNA samples for analysis by next-generation sequencing. We used a set of 96 barcoded adapters for tagmentation to barcode the RT-LAMP reaction products in each 96-well plate. After tagmentation, all barcoded fragments from each plate were pooled and size-selected by bead purification to remove excess adapters. A second set of barcoded primers, one per plate-pool, was then used to amplify the tagmented RT-LAMP fragments. Last, all amplified pools were combined for analysis using one next-generation sequencing run where the origin of each DNA fragment was specified by the two barcodes (Fig. 4A)."}