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PMC:7574920 / 52804-55213 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T191 599-602 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T192 998-1001 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T431 292-293 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T432 410-412 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T433 740-744 http://purl.obolibrary.org/obo/PR_000002979 denotes TAPS
T434 808-809 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T435 857-863 http://purl.obolibrary.org/obo/CLO_0009382 denotes Toledo
T436 955-956 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T437 1051-1052 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T438 1611-1612 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T439 1992-1995 http://purl.obolibrary.org/obo/CLO_0001562 denotes a 2
T440 1992-1995 http://purl.obolibrary.org/obo/CLO_0001563 denotes a 2
T441 2162-2163 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T442 2193-2194 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T443 2284-2286 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T444 2306-2308 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T445 2360-2362 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T75557 196-200 Chemical denotes tris http://purl.obolibrary.org/obo/CHEBI_9754
T83003 201-204 Chemical denotes HCl http://purl.obolibrary.org/obo/CHEBI_17883
T99414 455-459 Chemical denotes Tris http://purl.obolibrary.org/obo/CHEBI_9754
T12523 460-463 Chemical denotes HCl http://purl.obolibrary.org/obo/CHEBI_17883
T47167 599-602 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T6045 671-677 Chemical denotes buffer http://purl.obolibrary.org/obo/CHEBI_35225
T74345 686-690 Chemical denotes tris http://purl.obolibrary.org/obo/CHEBI_9754
T27218 691-704 Chemical denotes hydroxymethyl http://purl.obolibrary.org/obo/CHEBI_24712
T25862 705-716 Chemical denotes methylamino http://purl.obolibrary.org/obo/CHEBI_44209
T6351 733-737 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T29057 762-767 Chemical denotes MgCl2 http://purl.obolibrary.org/obo/CHEBI_6636
T54464 948-951 Chemical denotes SDS http://purl.obolibrary.org/obo/CHEBI_8984
T50580 998-1001 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T56525 1211-1216 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T73443 1421-1428 Chemical denotes ethanol http://purl.obolibrary.org/obo/CHEBI_16236
T70592 1485-1489 Chemical denotes tris http://purl.obolibrary.org/obo/CHEBI_9754
T8179 1490-1493 Chemical denotes HCl http://purl.obolibrary.org/obo/CHEBI_17883
T97460 1997-2004 Chemical denotes agarose http://purl.obolibrary.org/obo/CHEBI_2511
T41618 2005-2009 Chemical denotes tris http://purl.obolibrary.org/obo/CHEBI_9754
T95865 2010-2017 Chemical denotes acetate http://purl.obolibrary.org/obo/CHEBI_30089|http://purl.obolibrary.org/obo/CHEBI_47622
T15569 2018-2022 Chemical denotes EDTA http://purl.obolibrary.org/obo/CHEBI_42191|http://purl.obolibrary.org/obo/CHEBI_64755

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id tao:has_standard_notation
372 206-208 Gene denotes pH Gene:5053
373 308-319 Species denotes Transposons Tax:2387
374 196-200 Chemical denotes tris
375 201-204 Chemical denotes HCl MESH:D006851
376 948-951 Chemical denotes SDS MESH:D012967
377 1211-1216 Chemical denotes water MESH:D014867
378 1421-1428 Chemical denotes ethanol MESH:D000431
379 1485-1493 Chemical denotes tris-HCl
380 1997-2004 Chemical denotes agarose MESH:D012685
381 2005-2017 Chemical denotes tris-acetate
382 2018-2022 Chemical denotes EDTA MESH:D004492
383 740-744 Disease denotes TAPS
384 349-353 Mutation denotes E54K p.E54K
385 355-360 Mutation denotes L372P p.L372P

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T297 574-576 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T298 1548-1550 http://purl.obolibrary.org/obo/GO_0001171 denotes RT

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T6 345-348 GlycoEpitope denotes Tn5 http://www.glycoepitope.jp/epitopes/AN0083
T7 1569-1572 GlycoEpitope denotes Tn5 http://www.glycoepitope.jp/epitopes/AN0083

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T385 0-307 Sentence denotes In detail, transposon adapters containing well-defining barcodes and unique molecular identifiers (UMIs) were annealed by mixing 25 μM oligos (P5-UMI-xi5001…5096-ME.fw, Tn5hY-Rd2-Wat-SC3) in 5 μM tris-HCl (pH 8), incubating at 99°C for 5 min, and slowly cooling down to 20°C within 15 min in a thermocycler.
T386 308-520 Sentence denotes Transposons were assembled by mixing Tn5(E54K, L372P) transposase (100 ng/μl) [purified according to (41)] with 1.25 μM annealed adapters in 50 mM Tris-HCl (pH 7.5) and incubating the reaction for 1 hour at 23°C.
T387 521-865 Sentence denotes Tagmentation was carried out by mixing 1.2 μl of the RT-LAMP product (~200 ng DNA) with 1.5 μl of loaded transposase in freshly prepared tagmentation buffer [10 mM [tris(hydroxymethyl)methylamino]propanesulfonic acid) (TAPS)] (pH 8.5), 5 mM MgCl2, and 10% (v/v) dimethylformamide] using a Liquidator 96 Manual Pipetting System (Mettler Toledo).
T388 866-914 Sentence denotes The reactions were incubated at 55°C for 10 min.
T389 915-987 Sentence denotes Reactions were stopped by adding SDS to a final concentration of 0.033%.
T390 988-1154 Sentence denotes Tagmented DNA of each plate was pooled and size-selected using a two-step AMPureXP bead (Beckman Coulter) purification to target for fragments between 300 and 600 bp.
T391 1155-1271 Sentence denotes First, 50 μl of pooled reaction was mixed with 50 μl of water and bound to 55 μl of beads to remove large fragments.
T392 1272-1501 Sentence denotes To further remove small fragments, the supernatant of this reaction was added to 25 μl of fresh beads and further purified using two washes with 80% ethanol before the samples were finally eluted in 10 μl of 5 mM tris-HCl (pH 8).
T393 1502-1896 Sentence denotes One PCR per plate with 1 μl of the eluate and RT-LAMP–specific and Tn5-adapter–specific primers (P7nxt-GeneN-A-LBrc and P7-xi7001..7016, P5.fw) was performed using NEBNext Q5 HotStart polymerase (New England Biolabs) with two cycles at 62°C for annealing and 90 s elongation, followed by two cycles at 65°C for annealing and 90 s elongation, and 13 cycles at 72°C annealing and 90 s elongation.
T394 1897-2068 Sentence denotes All PCR reactions were combined and 19% of this pool was size-selected for 400 to 550 bp using a 2% agarose/tris-acetate-EDTA gel and column purification (Macherey-Nagel).
T395 2069-2409 Sentence denotes The final sequencing library was quantified by qPCR (New England Biolabs) and sequenced with a paired-end sequencing run on a NextSeq 550 machine (Illumina) with 20% phiX spike-in and 136 cycles for the first read, 11 cycles to read the 11-nt-long plate index (i7) and 20 cycles to read the 11-nt-long well index (i5) and the 9-nt-long UMI.