PMC:7252096 / 94975-97018
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T1068 | 9-11 | Body_part | denotes | v1 | http://purl.org/sig/ont/fma/fma13444|http://purl.org/sig/ont/fma/fma68614 |
| T1070 | 79-84 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T1071 | 108-113 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T1072 | 198-203 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T1073 | 739-743 | Body_part | denotes | mRNA | http://purl.org/sig/ont/fma/fma67122 |
| T1074 | 763-767 | Body_part | denotes | mRNA | http://purl.org/sig/ont/fma/fma67122 |
| T1075 | 1516-1519 | Body_part | denotes | DNA | http://purl.org/sig/ont/fma/fma74412 |
| T1076 | 1578-1581 | Body_part | denotes | DNA | http://purl.org/sig/ont/fma/fma74412 |
| T1077 | 1905-1907 | 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 |
|---|---|---|---|---|---|
| T368 | 1224-1226 | Disease | denotes | XP | http://purl.obolibrary.org/obo/MONDO_0019600 |
| T369 | 1728-1730 | Disease | denotes | XP | http://purl.obolibrary.org/obo/MONDO_0019600 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T1575 | 79-84 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1576 | 108-113 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1577 | 158-159 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1578 | 198-203 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1579 | 353-354 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1580 | 384-392 | http://purl.obolibrary.org/obo/UBERON_0000158 | denotes | membrane |
| T1581 | 425-426 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1582 | 470-471 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1583 | 850-851 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1584 | 973-974 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1585 | 1068-1070 | http://purl.obolibrary.org/obo/CLO_0001407 | denotes | 52 |
| T1586 | 1257-1258 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1587 | 1615-1617 | http://purl.obolibrary.org/obo/CLO_0008426 | denotes | pg |
| T1588 | 1758-1759 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1589 | 1875-1876 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1590 | 1930-1931 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T48419 | 179-183 | Chemical | denotes | PDMS | http://purl.obolibrary.org/obo/CHEBI_31498|http://purl.obolibrary.org/obo/CHEBI_61468 |
| T3587 | 240-244 | Chemical | denotes | PDMS | http://purl.obolibrary.org/obo/CHEBI_31498|http://purl.obolibrary.org/obo/CHEBI_61468 |
| T62366 | 370-383 | Chemical | denotes | polycarbonate | http://purl.obolibrary.org/obo/CHEBI_53201 |
| T163 | 478-484 | Chemical | denotes | buffer | http://purl.obolibrary.org/obo/CHEBI_35225 |
| T46753 | 506-517 | Chemical | denotes | thiocyanate | http://purl.obolibrary.org/obo/CHEBI_18022 |
| T165 | 527-531 | Chemical | denotes | EDTA | http://purl.obolibrary.org/obo/CHEBI_42191|http://purl.obolibrary.org/obo/CHEBI_64755 |
| T167 | 536-556 | Chemical | denotes | beta-mercaptoethanol | http://purl.obolibrary.org/obo/CHEBI_41218 |
| T53678 | 536-540 | Chemical | denotes | beta | http://purl.obolibrary.org/obo/CHEBI_10545 |
| T169 | 651-657 | Chemical | denotes | buffer | http://purl.obolibrary.org/obo/CHEBI_35225 |
| T1866 | 669-673 | Chemical | denotes | NaCl | http://purl.obolibrary.org/obo/CHEBI_26710 |
| T88001 | 941-947 | Chemical | denotes | buffer | http://purl.obolibrary.org/obo/CHEBI_35225 |
| T88936 | 962-971 | Chemical | denotes | inhibitor | http://purl.obolibrary.org/obo/CHEBI_35222 |
| T61760 | 994-1009 | Chemical | denotes | oligonucleotide | http://purl.obolibrary.org/obo/CHEBI_7754 |
| T67601 | 1015-1018 | Chemical | denotes | PEG | http://purl.obolibrary.org/obo/CHEBI_46793 |
| T97228 | 1516-1519 | Chemical | denotes | DNA | http://purl.obolibrary.org/obo/CHEBI_16991 |
| T80987 | 1578-1581 | Chemical | denotes | DNA | http://purl.obolibrary.org/obo/CHEBI_16991 |
| T43332 | 1996-2001 | Chemical | denotes | bases | http://purl.obolibrary.org/obo/CHEBI_22695 |
| T97733 | 2014-2019 | Chemical | denotes | bases | http://purl.obolibrary.org/obo/CHEBI_22695 |
| T75455 | 2037-2042 | Chemical | denotes | bases | http://purl.obolibrary.org/obo/CHEBI_22695 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T75 | 472-477 | http://purl.obolibrary.org/obo/GO_0019835 | denotes | lysis |
| T76 | 867-888 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | reverse transcription |
| T77 | 875-888 | http://purl.obolibrary.org/obo/GO_0006351 | denotes | transcription |
| T78 | 923-936 | http://purl.obolibrary.org/obo/GO_0003968 | denotes | Transcriptase |
| T79 | 923-936 | http://purl.obolibrary.org/obo/GO_0003899 | denotes | Transcriptase |
| T80 | 1113-1122 | http://purl.obolibrary.org/obo/GO_0007586 | denotes | digestion |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T678 | 0-11 | Sentence | denotes | Seq-Well v1 |
| T679 | 12-71 | Sentence | denotes | Seq-Well was performed as described (Gierahn et al., 2017). |
| T680 | 72-190 | Sentence | denotes | Single cells were diluted to 15,000 cells in 200 μL RPMI + 10% FBS and deposited onto a pre-functionalized PDMS array. |
| T681 | 191-297 | Sentence | denotes | 15,000 cells were deposited onto the top of each PDMS array and let settle by gravity into distinct wells. |
| T682 | 298-393 | Sentence | denotes | The array was gently washed with PBS, and sealed using a functionalized polycarbonate membrane. |
| T683 | 394-609 | Sentence | denotes | Seq-Well arrays were sealed in a dry 37°C oven for 40 min, and submerged in a lysis buffer containing guanidium thiocyanate (Sigma), EDTA, 1% beta-mercaptoethanol and sarkosyl (Sigma) for 20 min at room temperature. |
| T684 | 610-1100 | Sentence | denotes | Arrays were transferred to hybridization buffer containing NaCl (Fisher Scientific) and agitated for 40 min at room temperature, mRNA capture beads with mRNA hybridized were collected from each Seq-Well array, and beads were resuspended in a master mix for reverse transcription containing Maxima H Minus Reverse Transcriptase and buffer, dNTPs, RNase inhibitor, a 5′ template switch oligonucleotide, and PEG for 30 min at room temperature, and overnight at 52°C with end-over-end rotation. |
| T685 | 1101-1161 | Sentence | denotes | Exonuclease digestion and PCR were carried out as described. |
| T686 | 1162-1296 | Sentence | denotes | Post-whole transcriptome amplification workup involved AMPure XP SPRI bead cleanup occurred at a 0.6 x volume ratio, followed by 0.8x. |
| T687 | 1297-1460 | Sentence | denotes | Library size was analyzed using an Agilent Tapestation hsD5000 kit, confirming the expected peak at ∼1000 bp, and absence of smaller peaks corresponding to primer. |
| T688 | 1461-1669 | Sentence | denotes | Libraries were quantified using Qubit High-Sensitivity DNA kit and prepared for Illumina sequencing using Nextera XT DNA Sample Preparation kit using 900 pg of cDNA library as input to tagmentation reactions. |
| T689 | 1670-1798 | Sentence | denotes | Amplified final libraries were purified twice with AMPure XP SPRI beads as before, with a volume ratio of 0.6x followed by 0.8x. |
| T690 | 1799-1992 | Sentence | denotes | Libraries from 2-3 Seq-Well arrays were pooled and sequenced together using a NextSeq 500/550 High Output v2 kit (75 cycles) using a paired end read structure with custom read 1 primer: read 1: |
| T691 | 1993-2010 | Sentence | denotes | 20 bases, read 2: |
| T692 | 2011-2034 | Sentence | denotes | 50 bases, read 1 index: |
| T693 | 2035-2043 | Sentence | denotes | 8 bases. |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 2590 | 124-128 | Chemical | denotes | RPMI | |
| 2591 | 331-334 | Chemical | denotes | PBS | MESH:D007854 |
| 2592 | 496-517 | Chemical | denotes | guanidium thiocyanate | |
| 2593 | 527-531 | Chemical | denotes | EDTA | MESH:D004492 |
| 2594 | 536-556 | Chemical | denotes | beta-mercaptoethanol | |
| 2595 | 561-569 | Chemical | denotes | sarkosyl | MESH:C025231 |
| 2596 | 669-673 | Chemical | denotes | NaCl | MESH:D012965 |
| 2597 | 949-954 | Chemical | denotes | dNTPs | |
| 2598 | 994-1009 | Chemical | denotes | oligonucleotide | MESH:D009841 |
| 2599 | 1015-1018 | Chemical | denotes | PEG | MESH:D011092 |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32413319-28192419-20790572 | 65-69 | 28192419 | denotes | 2017 |