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PMC:7252096 / 98943-100490 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 11-14 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T2 112-115 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T3 166-169 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T4 394-398 Body_part denotes mRNA http://purl.org/sig/ont/fma/fma67122
T5 879-882 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T6 1033-1036 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T7 1103-1107 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T8 1309-1312 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T9 1367-1370 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T10 1458-1460 Body_part denotes v2 http://purl.org/sig/ont/fma/fma13443|http://purl.org/sig/ont/fma/fma68615

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T370 770-772 Disease denotes XP http://purl.obolibrary.org/obo/MONDO_0019600
T371 1216-1218 Disease denotes XP http://purl.obolibrary.org/obo/MONDO_0019600

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 72-76 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T2 208-209 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3 335-336 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 441-442 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 572-573 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T6 722-724 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T7 787-788 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 860-861 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 1081-1083 http://purl.obolibrary.org/obo/CLO_0008426 denotes pg
T10 1103-1107 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T11 1233-1234 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 1290-1291 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T412 284-293 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T12068 491-497 Chemical denotes buffer http://purl.obolibrary.org/obo/CHEBI_35225
T8993 519-524 Chemical denotes MgCl2 http://purl.obolibrary.org/obo/CHEBI_6636
T85647 534-541 Chemical denotes Betaine http://purl.obolibrary.org/obo/CHEBI_17750
T67564 557-566 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T80309 593-608 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T42106 879-882 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T37502 1033-1036 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T49482 1309-1312 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T12825 1367-1370 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 400-421 http://purl.obolibrary.org/obo/GO_0001171 denotes Reverse transcription
T2 408-421 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T712 0-102 Sentence denotes Population RNA-seq was performed as described (Ordovas-Montanes et al., 2018, Trombetta et al., 2014).
T713 103-399 Sentence denotes Briefly, RNA from population lysates was purified using AMPure RNA Clean Spri beads (Beckman Coulter) at a 2.2x volume ratio, and mixed with oligo-dT primer, dNTPs (NEB), and RNase inhibitor (Fisher Scientific) at 72°C for 3 min on a thermal cycler to anneal the 3′ primer to polyadenylated mRNA.
T714 400-732 Sentence denotes Reverse transcription was carried out in a master mix of Maxima RNaseH-minus RT enzyme and buffer (Fisher Scientific), MgCl2 (Sigma), Betaine (Sigma), RNase inhibitor, and a 5′ template switch oligonucleotide, and PCR was carried out using KAPA HiFi HotStart ReadyMix (Kapa Biosystems) and IS PCR primer and amplified for 18 cycles.
T715 733-827 Sentence denotes Libraries were purified using AMPure XP SPRI beads at a volume ratio of 0.8x followed by 0.9x.
T716 828-972 Sentence denotes Library size was assessed using a High-Sensitivity DNA chip (Agilent Bioanalyzer), confirming the expected size distribution of ∼1,000-2,000 bp.
T717 973-1173 Sentence denotes Tagmentation reactions were carried out with the Nextera XT DNA Sample Preparation Kit (Illumina) using 250 pg of cDNA per single cell as input, with modified manufacturer’s instructions as described.
T718 1174-1388 Sentence denotes Libraries were purified twice with AMPure XP SPRI beads at a volume ratio of 0.9x, size distribution assessed using a High Sensitivity DNA chip (Agilent Bioanalyzer) and Qubit High-Sensitivity DNA kit (Invitrogen).
T719 1389-1547 Sentence denotes Libraries were pooled and sequenced using NextSeq500/550 High Output v2 kits (75 cycles, Illumina) using 30-30 paired end sequencing with 8-mer dual indexing.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
2627 261-266 Chemical denotes dNTPs
2628 519-524 Chemical denotes MgCl2 MESH:D015636
2629 534-541 Chemical denotes Betaine MESH:D001622
2630 593-608 Chemical denotes oligonucleotide MESH:D009841
2631 645-667 Disease denotes HiFi HotStart ReadyMix

2_test

Id Subject Object Predicate Lexical cue
32413319-30135581-20790574 72-76 30135581 denotes 2018