PMC:7252096 / 118463-120734 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T155 86-90 Body_part denotes mRNA http://purl.org/sig/ont/fma/fma67122
T156 134-138 Body_part denotes mRNA http://purl.org/sig/ont/fma/fma67122
T157 153-157 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T158 408-410 Body_part denotes v1 http://purl.org/sig/ont/fma/fma13444|http://purl.org/sig/ont/fma/fma68614
T160 510-514 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T161 598-616 Body_part denotes inferior turbinate http://purl.org/sig/ont/fma/fma54736
T162 662-664 Body_part denotes v1 http://purl.org/sig/ont/fma/fma13444|http://purl.org/sig/ont/fma/fma68614
T164 824-826 Body_part denotes v1 http://purl.org/sig/ont/fma/fma13444|http://purl.org/sig/ont/fma/fma68614
T166 912-916 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T167 1108-1112 Body_part denotes mRNA http://purl.org/sig/ont/fma/fma67122
T168 1127-1131 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T169 1204-1209 Body_part denotes ileum http://purl.org/sig/ont/fma/fma7208
T170 1210-1215 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T171 1262-1266 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T172 1328-1332 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T173 1347-1352 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T174 1490-1494 Body_part denotes mRNA http://purl.org/sig/ont/fma/fma67122
T175 1528-1532 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T176 1683-1687 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T177 1844-1849 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T178 1918-1922 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T179 2164-2169 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T255 1204-1209 Body_part denotes ileum http://purl.obolibrary.org/obo/UBERON_0002116

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T235 104-105 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T236 149-157 http://purl.obolibrary.org/obo/CLO_0008190 denotes per cell
T237 162-163 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T238 209-212 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T239 213-214 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T240 510-514 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T241 912-916 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T242 1123-1131 http://purl.obolibrary.org/obo/CLO_0008190 denotes per cell
T243 1133-1134 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T244 1190-1195 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T245 1196-1203 http://purl.obolibrary.org/obo/NCBITaxon_9443 denotes primate
T246 1204-1209 http://purl.obolibrary.org/obo/UBERON_0002116 denotes ileum
T247 1210-1215 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T248 1220-1221 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T249 1258-1266 http://purl.obolibrary.org/obo/CLO_0008190 denotes per cell
T250 1324-1332 http://purl.obolibrary.org/obo/CLO_0008190 denotes per cell
T251 1347-1352 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T252 1410-1411 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T253 1434-1436 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T254 1528-1532 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T255 1683-1687 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T256 1844-1849 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T257 1918-1922 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T258 2012-2013 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T259 2038-2039 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T260 2164-2169 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T261 2252-2253 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T40879 91-99 Chemical denotes molecule http://purl.obolibrary.org/obo/CHEBI_25367
T78056 139-148 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T35798 476-484 Chemical denotes molecule http://purl.obolibrary.org/obo/CHEBI_25367
T3501 540-542 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T914 678-680 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T21728 717-719 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T55329 843-845 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T49729 1113-1122 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T70596 1248-1257 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T14582 1314-1323 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T92850 1495-1503 Chemical denotes molecule http://purl.obolibrary.org/obo/CHEBI_25367

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T16 223-236 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T17 998-1011 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T18 1703-1716 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T19 1788-1798 http://purl.obolibrary.org/obo/GO_0006351 denotes transcript
T20 1872-1885 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T846 0-199 Sentence denotes We began by quantifying how likely we are to capture and transcribe at least one ACE2 mRNA molecule, as a function of the number ACE2 mRNA molecules per cell and a protocol’s efficiency (Figure S6A).
T847 200-566 Sentence denotes Drop-Seq has a capture/transcription efficiency of ∼10% (as estimated using ERCC spike ins; see (Macosko et al., 2015), and the experimental platforms used in this study are either equivalent (e.g., Seq-Well v1, (Gierahn et al., 2017) or superior (e.g., 10-fold better unique molecule detection, 5-fold better gene detection using Seq-Well S3;(Hughes et al., 2019)).
T848 567-694 Sentence denotes Most relevant to this context, inferior turbinate scrapings were processed using both Seq-Well v1 and Seq-Well S3 (Figure S3B).
T849 695-814 Sentence denotes Importantly, Seq-Well S3 provided > two-fold increase in the detection frequency of rare ACE2 transcripts (i.e., ACE2+:
T850 815-1023 Sentence denotes 4.7% for v1 versus 9.8% for S3), making it reasonable to expect that such improvements in single-cell experimental technologies have yielded corresponding improvements in capture and transcription efficiency.
T851 1024-1533 Sentence denotes Based on Drop-Seq’s 10% efficiency, even if ACE2 is expressed at the low level of 5 mRNA molecules per cell (a reasonable order-of-magnitude estimate, given that non-human primate ileum cells had a maximum of 10 ACE2 unique molecules per cell observed via sequencing and an average of 1.93 molecules per cell in expressing cells, see Figures 3B and 3C), our experimental platforms have a minimum likelihood of 41% to capture and reverse transcribe at least one ACE2 mRNA molecule in any given individual cell.
T852 1534-1775 Sentence denotes This likelihood rapidly increases if we estimate higher efficiencies for improved scRNA-seq technologies (e.g., 67% likelihood within any individual cell at 20% capture/transcription efficiency, 76% likelihood at 25% efficiency, Figure S6A).
T853 1776-2083 Sentence denotes Thus, while transcript drop-out may reduce the fraction of positive cells, with the capture and transcription efficiencies of improved single-cell technologies, the impact is likely to be minor (reads are likely underestimated by up to a factor of ∼2.5x), given a sufficient depth of sequencing (see below).
T854 2084-2271 Sentence denotes We note that this impacts both clusters deemed to contain and not contain ACE2+ cells, and suggests our percentages are likely lower bounds for true expression (within a factor of ∼2.5x).

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
2824 81-85 Gene denotes ACE2 Gene:59272
2825 129-133 Gene denotes ACE2 Gene:59272
2826 784-788 Gene denotes ACE2 Gene:59272
2827 808-812 Gene denotes ACE2 Gene:59272
2828 1068-1072 Gene denotes ACE2 Gene:59272
2829 1236-1240 Gene denotes ACE2 Gene:59272
2830 1485-1489 Gene denotes ACE2 Gene:59272
2831 2158-2162 Gene denotes ACE2 Gene:59272
2832 281-286 Gene denotes spike Gene:43740568
2833 1190-1195 Species denotes human Tax:9606

2_test

Id Subject Object Predicate Lexical cue
32413319-26000488-20790592 313-317 26000488 denotes 2015
32413319-28192419-20790593 429-433 28192419 denotes 2017