PMC:7252096 / 97020-97588 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T1079","span":{"begin":67,"end":69},"obj":"Body_part"}],"attributes":[{"id":"A1079","pred":"fma_id","subj":"T1079","obj":"http://purl.org/sig/ont/fma/fma13444"},{"id":"A1080","pred":"fma_id","subj":"T1079","obj":"http://purl.org/sig/ont/fma/fma68614"}],"text":"Seq-Well S3\nSeq-Well S3 modified the following protocol steps from v1, above (Hughes et al., 2019). First, hybridization buffer was supplanted with 8% (v/v) polyethylene glycol (PEG, Sigma). Second, after exonuclease digestion, bead-associated cDNA was denatured for 5 min in 0.2 mM NaOH with end over end rotation. Next, beads were washed with TE + 0.01% tween-20, and second strand synthesis was carried out by resuspending beads in a master mix containing Klenow Fragment (NEB), dNTPs, PEG, and the dN-SMRT oligonucleotide to enable random priming off of the beads."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T1591","span":{"begin":345,"end":347},"obj":"http://purl.obolibrary.org/obo/CLO_0009287"},{"id":"T1592","span":{"begin":435,"end":436},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"Seq-Well S3\nSeq-Well S3 modified the following protocol steps from v1, above (Hughes et al., 2019). First, hybridization buffer was supplanted with 8% (v/v) polyethylene glycol (PEG, Sigma). Second, after exonuclease digestion, bead-associated cDNA was denatured for 5 min in 0.2 mM NaOH with end over end rotation. Next, beads were washed with TE + 0.01% tween-20, and second strand synthesis was carried out by resuspending beads in a master mix containing Klenow Fragment (NEB), dNTPs, PEG, and the dN-SMRT oligonucleotide to enable random priming off of the beads."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T64977","span":{"begin":9,"end":11},"obj":"Chemical"},{"id":"T79129","span":{"begin":21,"end":23},"obj":"Chemical"},{"id":"T9601","span":{"begin":121,"end":127},"obj":"Chemical"},{"id":"T7108","span":{"begin":157,"end":176},"obj":"Chemical"},{"id":"T23785","span":{"begin":157,"end":169},"obj":"Chemical"},{"id":"T40008","span":{"begin":170,"end":176},"obj":"Chemical"},{"id":"T37602","span":{"begin":178,"end":181},"obj":"Chemical"},{"id":"T47327","span":{"begin":283,"end":287},"obj":"Chemical"},{"id":"T51634","span":{"begin":345,"end":347},"obj":"Chemical"},{"id":"T68917","span":{"begin":489,"end":492},"obj":"Chemical"},{"id":"T99070","span":{"begin":502,"end":504},"obj":"Chemical"},{"id":"T16126","span":{"begin":510,"end":525},"obj":"Chemical"}],"attributes":[{"id":"A22721","pred":"chebi_id","subj":"T64977","obj":"http://purl.obolibrary.org/obo/CHEBI_29388"},{"id":"A6232","pred":"chebi_id","subj":"T79129","obj":"http://purl.obolibrary.org/obo/CHEBI_29388"},{"id":"A15948","pred":"chebi_id","subj":"T9601","obj":"http://purl.obolibrary.org/obo/CHEBI_35225"},{"id":"A10311","pred":"chebi_id","subj":"T7108","obj":"http://purl.obolibrary.org/obo/CHEBI_46793"},{"id":"A33040","pred":"chebi_id","subj":"T23785","obj":"http://purl.obolibrary.org/obo/CHEBI_53226"},{"id":"A99509","pred":"chebi_id","subj":"T23785","obj":"http://purl.obolibrary.org/obo/CHEBI_53227"},{"id":"A34813","pred":"chebi_id","subj":"T23785","obj":"http://purl.obolibrary.org/obo/CHEBI_60034"},{"id":"A74106","pred":"chebi_id","subj":"T40008","obj":"http://purl.obolibrary.org/obo/CHEBI_13643"},{"id":"A89921","pred":"chebi_id","subj":"T37602","obj":"http://purl.obolibrary.org/obo/CHEBI_46793"},{"id":"A15080","pred":"chebi_id","subj":"T47327","obj":"http://purl.obolibrary.org/obo/CHEBI_32145"},{"id":"A56775","pred":"chebi_id","subj":"T51634","obj":"http://purl.obolibrary.org/obo/CHEBI_74857"},{"id":"A85637","pred":"chebi_id","subj":"T68917","obj":"http://purl.obolibrary.org/obo/CHEBI_46793"},{"id":"A64603","pred":"chebi_id","subj":"T99070","obj":"http://purl.obolibrary.org/obo/CHEBI_33793"},{"id":"A67912","pred":"chebi_id","subj":"T16126","obj":"http://purl.obolibrary.org/obo/CHEBI_7754"}],"text":"Seq-Well S3\nSeq-Well S3 modified the following protocol steps from v1, above (Hughes et al., 2019). First, hybridization buffer was supplanted with 8% (v/v) polyethylene glycol (PEG, Sigma). Second, after exonuclease digestion, bead-associated cDNA was denatured for 5 min in 0.2 mM NaOH with end over end rotation. Next, beads were washed with TE + 0.01% tween-20, and second strand synthesis was carried out by resuspending beads in a master mix containing Klenow Fragment (NEB), dNTPs, PEG, and the dN-SMRT oligonucleotide to enable random priming off of the beads."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T81","span":{"begin":217,"end":226},"obj":"http://purl.obolibrary.org/obo/GO_0007586"},{"id":"T82","span":{"begin":384,"end":393},"obj":"http://purl.obolibrary.org/obo/GO_0009058"},{"id":"T83","span":{"begin":459,"end":474},"obj":"http://purl.obolibrary.org/obo/GO_0003887"}],"text":"Seq-Well S3\nSeq-Well S3 modified the following protocol steps from v1, above (Hughes et al., 2019). First, hybridization buffer was supplanted with 8% (v/v) polyethylene glycol (PEG, Sigma). Second, after exonuclease digestion, bead-associated cDNA was denatured for 5 min in 0.2 mM NaOH with end over end rotation. Next, beads were washed with TE + 0.01% tween-20, and second strand synthesis was carried out by resuspending beads in a master mix containing Klenow Fragment (NEB), dNTPs, PEG, and the dN-SMRT oligonucleotide to enable random priming off of the beads."}

{"project":"LitCovid-sentences","denotations":[{"id":"T694","span":{"begin":0,"end":11},"obj":"Sentence"},{"id":"T695","span":{"begin":12,"end":99},"obj":"Sentence"},{"id":"T696","span":{"begin":100,"end":190},"obj":"Sentence"},{"id":"T697","span":{"begin":191,"end":315},"obj":"Sentence"},{"id":"T698","span":{"begin":316,"end":568},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Seq-Well S3\nSeq-Well S3 modified the following protocol steps from v1, above (Hughes et al., 2019). First, hybridization buffer was supplanted with 8% (v/v) polyethylene glycol (PEG, Sigma). Second, after exonuclease digestion, bead-associated cDNA was denatured for 5 min in 0.2 mM NaOH with end over end rotation. Next, beads were washed with TE + 0.01% tween-20, and second strand synthesis was carried out by resuspending beads in a master mix containing Klenow Fragment (NEB), dNTPs, PEG, and the dN-SMRT oligonucleotide to enable random priming off of the beads."}

{"project":"LitCovid-PubTator","denotations":[{"id":"2608","span":{"begin":505,"end":509},"obj":"Gene"},{"id":"2609","span":{"begin":157,"end":176},"obj":"Chemical"},{"id":"2610","span":{"begin":178,"end":181},"obj":"Chemical"},{"id":"2611","span":{"begin":283,"end":287},"obj":"Chemical"},{"id":"2612","span":{"begin":356,"end":364},"obj":"Chemical"},{"id":"2613","span":{"begin":482,"end":487},"obj":"Chemical"},{"id":"2614","span":{"begin":489,"end":492},"obj":"Chemical"},{"id":"2615","span":{"begin":510,"end":525},"obj":"Chemical"}],"attributes":[{"id":"A2608","pred":"tao:has_database_id","subj":"2608","obj":"Gene:9612"},{"id":"A2609","pred":"tao:has_database_id","subj":"2609","obj":"MESH:D011092"},{"id":"A2610","pred":"tao:has_database_id","subj":"2610","obj":"MESH:D011092"},{"id":"A2612","pred":"tao:has_database_id","subj":"2612","obj":"MESH:D011136"},{"id":"A2614","pred":"tao:has_database_id","subj":"2614","obj":"MESH:D011092"},{"id":"A2615","pred":"tao:has_database_id","subj":"2615","obj":"MESH:D009841"}],"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":"Seq-Well S3\nSeq-Well S3 modified the following protocol steps from v1, above (Hughes et al., 2019). First, hybridization buffer was supplanted with 8% (v/v) polyethylene glycol (PEG, Sigma). Second, after exonuclease digestion, bead-associated cDNA was denatured for 5 min in 0.2 mM NaOH with end over end rotation. Next, beads were washed with TE + 0.01% tween-20, and second strand synthesis was carried out by resuspending beads in a master mix containing Klenow Fragment (NEB), dNTPs, PEG, and the dN-SMRT oligonucleotide to enable random priming off of the beads."}