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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T190 220-223 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T191 892-895 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T192 1291-1294 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T193 3000-3006 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T194 3098-3104 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T195 3241-3247 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T196 3793-3797 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T197 5098-5101 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T105 2979-2987 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T106 3780-3788 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T430 111-112 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T431 585-586 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T432 703-705 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T433 1033-1037 http://purl.obolibrary.org/obo/PR_000002979 denotes TAPS
T434 1101-1102 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T435 1150-1156 http://purl.obolibrary.org/obo/CLO_0009382 denotes Toledo
T436 1248-1249 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T437 1344-1345 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T438 1904-1905 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T439 2285-2288 http://purl.obolibrary.org/obo/CLO_0001562 denotes a 2
T440 2285-2288 http://purl.obolibrary.org/obo/CLO_0001563 denotes a 2
T441 2455-2456 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T442 2486-2487 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T443 2577-2579 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T444 2599-2601 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T445 2653-2655 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T446 3092-3097 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T447 3177-3179 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T448 3235-3240 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T449 3258-3259 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T450 3304-3305 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T451 3327-3328 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T452 3419-3420 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T453 3744-3745 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T454 3769-3770 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T455 3793-3797 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T456 4054-4057 http://purl.obolibrary.org/obo/PR_000001343 denotes aim
T457 4086-4087 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T458 4192-4197 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T459 4236-4237 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T460 4269-4274 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T461 4455-4456 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T462 4803-4804 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T63691 220-223 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T55476 289-291 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T75557 489-493 Chemical denotes tris http://purl.obolibrary.org/obo/CHEBI_9754
T83003 494-497 Chemical denotes HCl http://purl.obolibrary.org/obo/CHEBI_17883
T99414 748-752 Chemical denotes Tris http://purl.obolibrary.org/obo/CHEBI_9754
T12523 753-756 Chemical denotes HCl http://purl.obolibrary.org/obo/CHEBI_17883
T47167 892-895 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T6045 964-970 Chemical denotes buffer http://purl.obolibrary.org/obo/CHEBI_35225
T74345 979-983 Chemical denotes tris http://purl.obolibrary.org/obo/CHEBI_9754
T27218 984-997 Chemical denotes hydroxymethyl http://purl.obolibrary.org/obo/CHEBI_24712
T25862 998-1009 Chemical denotes methylamino http://purl.obolibrary.org/obo/CHEBI_44209
T6351 1026-1030 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T29057 1055-1060 Chemical denotes MgCl2 http://purl.obolibrary.org/obo/CHEBI_6636
T54464 1241-1244 Chemical denotes SDS http://purl.obolibrary.org/obo/CHEBI_8984
T50580 1291-1294 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T56525 1504-1509 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T73443 1714-1721 Chemical denotes ethanol http://purl.obolibrary.org/obo/CHEBI_16236
T70592 1778-1782 Chemical denotes tris http://purl.obolibrary.org/obo/CHEBI_9754
T8179 1783-1786 Chemical denotes HCl http://purl.obolibrary.org/obo/CHEBI_17883
T97460 2290-2297 Chemical denotes agarose http://purl.obolibrary.org/obo/CHEBI_2511
T41618 2298-2302 Chemical denotes tris http://purl.obolibrary.org/obo/CHEBI_9754
T95865 2303-2310 Chemical denotes acetate http://purl.obolibrary.org/obo/CHEBI_30089|http://purl.obolibrary.org/obo/CHEBI_47622
T15569 2311-2315 Chemical denotes EDTA http://purl.obolibrary.org/obo/CHEBI_42191|http://purl.obolibrary.org/obo/CHEBI_64755
T86686 3254-3256 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T89454 5098-5101 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id tao:has_standard_notation
372 499-501 Gene denotes pH Gene:5053
373 601-612 Species denotes Transposons Tax:2387
374 489-493 Chemical denotes tris
375 494-497 Chemical denotes HCl MESH:D006851
376 1241-1244 Chemical denotes SDS MESH:D012967
377 1504-1509 Chemical denotes water MESH:D014867
378 1714-1721 Chemical denotes ethanol MESH:D000431
379 1778-1786 Chemical denotes tris-HCl
380 2290-2297 Chemical denotes agarose MESH:D012685
381 2298-2310 Chemical denotes tris-acetate
382 2311-2315 Chemical denotes EDTA MESH:D004492
383 1033-1037 Disease denotes TAPS
384 642-646 Mutation denotes E54K p.E54K
385 648-653 Mutation denotes L372P p.L372P
388 3254-3265 Gene denotes S4, B and C Gene:6192
389 2979-2989 Species denotes SARS-CoV-2 Tax:2697049
392 3791-3792 Gene denotes N Gene:43740575
393 3780-3790 Species denotes SARS-CoV-2 Tax:2697049
395 5080-5083 Gene denotes S5B Gene:5711

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T295 77-79 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T296 220-237 http://purl.obolibrary.org/obo/GO_0006309 denotes DNA fragmentation
T297 867-869 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T298 1841-1843 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T299 3890-3892 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T300 4528-4530 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T301 5116-5118 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T302 5170-5172 http://purl.obolibrary.org/obo/GO_0001171 denotes RT

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T5 157-160 GlycoEpitope denotes Tn5 http://www.glycoepitope.jp/epitopes/AN0083
T6 638-641 GlycoEpitope denotes Tn5 http://www.glycoepitope.jp/epitopes/AN0083
T7 1862-1865 GlycoEpitope denotes Tn5 http://www.glycoepitope.jp/epitopes/AN0083

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T382 0-22 Sentence denotes LAMP-sequencing method
T383 23-243 Sentence denotes Sequencing libraries for detecting viral sequences in RT-LAMP products were prepared by a modified Anchor-Seq protocol (37, 40) using Tn5 transposase tagmentation instead of sonication for genomic DNA fragmentation (17).
T384 244-292 Sentence denotes The relevant primers are summarized in table S4.
T385 293-600 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 601-813 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 814-1158 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 1159-1207 Sentence denotes The reactions were incubated at 55°C for 10 min.
T389 1208-1280 Sentence denotes Reactions were stopped by adding SDS to a final concentration of 0.033%.
T390 1281-1447 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 1448-1564 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 1565-1794 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 1795-2189 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 2190-2361 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 2362-2702 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.
T396 2703-2816 Sentence denotes For trimming of the reads (i.e., removal of P7 Illumina adapter sequences), cutadapt (version 2.8) (42) was used.
T397 2817-2953 Sentence denotes For validation of the origin of the sequence of the LAMP product (fig. S4A), 107 reads were randomly selected and used for the analysis.
T398 2954-3091 Sentence denotes Reads were mapped to the SARS-CoV-2 reference genome (NC_045512.2) (43), using bwa-mem with default settings (version 0.7.17-r1188) (44).
T399 3092-3181 Sentence denotes Virus genome coverage was determined with the samtools depth command (version 1.10) (45).
T400 3182-3267 Sentence denotes Using bwa-mem, 80.6% of reads could be mapped to the virus genome (fig. S4, B and C).
T401 3268-3357 Sentence denotes To analyze the remaining sequences, a k-mer analysis using a custom script was performed.
T402 3358-3533 Sentence denotes Using 9-mers, this matched 93.5% of the nonmapped reads with a maximal Levenshtein distance of two to one of the LAMP primers or their reverse complement sequences (fig. S4D).
T403 3534-3630 Sentence denotes This is explained by the fact that LAMP products can consist of complex sequence rearrangements.
T404 3631-3743 Sentence denotes For classification of samples by LAMP-sequencing, reads were assigned to wells and counted using custom scripts.
T405 3744-3967 Sentence denotes A read was considered as a match to SARS-CoV-2 N gene if at least one of three short sequences (~13 nt, marked orange in fig. S4A) not covered by RT-LAMP primers was found in the read, otherwise it was counted as unmatched.
T406 3968-4085 Sentence denotes Sequencing reads were grouped by UMI and by position of the matched sequence with the aim of removing PCR duplicates.
T407 4086-4226 Sentence denotes A sample was considered if more than 200 total UMIs were observed and called positive if more than 10,000 virus-matching UMIs were observed.
T408 4227-4339 Sentence denotes There is a very wide gap in the number of virus-matching reads between positive and negative samples (fig. S5A):
T409 4340-4397 Sentence denotes The count is either below 7000 UMIs or above 45,000 UMIs.
T410 4398-4508 Sentence denotes This is why we placed the decision threshold for scoring a sample as LAMP-sequencing positive within this gap.
T411 4509-4798 Sentence denotes The fact that also RT-qPCR–negative samples give rise to some UMI counts containing viral sequences is explained by template switching of unattached adapters that remain in the reaction after tagmentation, but no cause for concern due to the wide gap between negative and positive samples.
T412 4799-4945 Sentence denotes For a few samples, we saw so few reads (less than 200 UMIs) that we suspected that the multiplexing had failed and excluded them from the results.
T413 4946-5124 Sentence denotes As most of these were in the same row of the same plate, we analyzed these samples after LAMP-sequencing by gel electrophoresis (fig. S5B) to check for DNA content after RT-LAMP.
T414 5125-5269 Sentence denotes We found that the gel results agree with the RT-LAMP outcome, indicating that the failure likely was caused later, probably during multiplexing.