PMC:7417788 / 75331-78047
Annnotations
LitCovid-PMC-OGER-BB
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T1513 | 61-66 | SO:0000150 | denotes | reads |
| T1514 | 111-117 | SO:0001505 | denotes | genome |
| T1515 | 429-435 | SO:0001026 | denotes | genome |
| T1516 | 490-492 | SO:0000028 | denotes | bp |
| T1517 | 613-615 | SO:0000028 | denotes | bp |
| T1518 | 648-650 | SO:0000028 | denotes | bp |
| T1519 | 1176-1181 | SO:0000150 | denotes | reads |
| T1520 | 1358-1365 | SO:0001026 | denotes | genomic |
| T1521 | 1549-1551 | SO:0000028 | denotes | bp |
| T1522 | 1778-1780 | SO:0000028 | denotes | bp |
| T1523 | 2553-2558 | SP_6;NCBITaxon:9606 | denotes | human |
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T553 | 111-117 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
| T554 | 234-238 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T555 | 324-329 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T556 | 429-435 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
| T557 | 757-761 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T558 | 1072-1076 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T559 | 1295-1299 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T560 | 1767-1771 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T561 | 2084-2088 | Body_part | denotes | Cell | http://purl.org/sig/ont/fma/fma68646 |
| T562 | 2187-2200 | Body_part | denotes | cell clusters | http://purl.org/sig/ont/fma/fma62807 |
| T563 | 2187-2191 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T564 | 2359-2363 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T565 | 2444-2448 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T42 | 1940-1945 | Body_part | denotes | Scale | http://purl.obolibrary.org/obo/UBERON_0002542 |
| T43 | 2187-2200 | Body_part | denotes | cell clusters | http://purl.obolibrary.org/obo/UBERON_0034922 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T142 | 409-412 | Disease | denotes | TSS | http://purl.obolibrary.org/obo/MONDO_0001881 |
| T143 | 503-506 | Disease | denotes | TSS | http://purl.obolibrary.org/obo/MONDO_0001881 |
| T144 | 540-543 | Disease | denotes | TSS | http://purl.obolibrary.org/obo/MONDO_0001881 |
| T145 | 625-628 | Disease | denotes | TSS | http://purl.obolibrary.org/obo/MONDO_0001881 |
| T146 | 698-701 | Disease | denotes | TSS | http://purl.obolibrary.org/obo/MONDO_0001881 |
| T147 | 2516-2519 | Disease | denotes | CIS | http://purl.obolibrary.org/obo/MONDO_0004647 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T1210 | 234-238 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T1211 | 277-278 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1212 | 284-290 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signal |
| T1213 | 324-329 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T1214 | 732-733 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1215 | 757-761 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T1216 | 826-827 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1217 | 842-848 | http://purl.obolibrary.org/obo/BFO_0000030 | denotes | object |
| T1218 | 1034-1035 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1219 | 1072-1076 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T1220 | 1101-1107 | http://purl.obolibrary.org/obo/BFO_0000030 | denotes | object |
| T1221 | 1126-1127 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1222 | 1295-1299 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T1223 | 1431-1432 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1224 | 1447-1453 | http://purl.obolibrary.org/obo/BFO_0000030 | denotes | object |
| T1225 | 1601-1602 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T1226 | 1767-1771 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T1227 | 2084-2088 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | Cell |
| T1228 | 2187-2200 | http://purl.obolibrary.org/obo/UBERON_0034922 | denotes | cell clusters |
| T1229 | 2359-2363 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T1230 | 2405-2413 | http://purl.obolibrary.org/obo/CLO_0001658 | denotes | activity |
| T1231 | 2444-2448 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T51166 | 2402-2404 | Chemical | denotes | TF | http://purl.obolibrary.org/obo/CHEBI_74862 |
| T166 | 2520-2522 | Chemical | denotes | BP | http://purl.obolibrary.org/obo/CHEBI_29865 |
| T84158 | 2635-2637 | Chemical | denotes | GC | http://purl.obolibrary.org/obo/CHEBI_73890 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T309 | 2402-2404 | http://purl.obolibrary.org/obo/GO_0000981 | denotes | TF |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T428 | 0-26 | Sentence | denotes | scATAC-seq data processing |
| T429 | 28-49 | Sentence | denotes | scATAC-seq processing |
| T430 | 50-185 | Sentence | denotes | scATAC-seq reads were aligned to the GRCh38 (hg38) reference genome and quantified using CellRanger-ATAC count (10x Genomics, v.1.0.0). |
| T431 | 187-213 | Sentence | denotes | scATAC-seq quality control |
| T432 | 214-395 | Sentence | denotes | To ensure that each cell was both adequately sequenced and had a high signal-to-background ratio, we filtered cells with less than 1,000 unique fragments and enrichment at TSSs < 8. |
| T433 | 396-544 | Sentence | denotes | To calculate TSS enrichment > 2, genome-wide Tn5-corrected insertions were aggregated ± 2,000 bp relative (TSS-strand-corrected) to each unique TSS. |
| T434 | 545-718 | Sentence | denotes | This profile was normalized to the mean accessibility ± 1,900–2,000 bp from the TSS, smoothed every 51 bp and the maximum smoothed value was reported as TSS enrichment in R. |
| T435 | 719-849 | Sentence | denotes | To construct a counts matrix for each cell by each feature (peaks), we read each fragment.tsv.gz fill into a GenomicRanges object. |
| T436 | 850-1019 | Sentence | denotes | For each Tn5 insertion, which can be thought of as the “start” and “end” of the ATAC fragments, we used findOverlaps to find all overlaps with the feature by insertions. |
| T437 | 1020-1146 | Sentence | denotes | Then we added a column with the unique id (integer) cell barcode to the overlaps object and fed this into a sparseMatrix in R. |
| T438 | 1147-1328 | Sentence | denotes | To calculate the fraction of reads/insertions in peaks, we used the colSums of the sparseMatrix and divided it by the number of insertions for each cell id barcode using table in R. |
| T439 | 1330-1373 | Sentence | denotes | scATAC-seq visualization in genomic regions |
| T440 | 1374-1459 | Sentence | denotes | To visualize scATAC-seq data, we read the fragments into a GenomicRanges object in R. |
| T441 | 1460-1588 | Sentence | denotes | We then computed sliding windows across each region we wanted to visualize for every 100 bp “slidingWindows (region, 100, 100)”. |
| T442 | 1589-1696 | Sentence | denotes | We computed a counts matrix for Tn5-corrected insertions as described above and then binarized this matrix. |
| T443 | 1697-1842 | Sentence | denotes | We then returned all non-zero indices (binarization) from the matrix (cell × 100-bp intervals) and plotted them in ggplot2 in R with “geom_tile”. |
| T444 | 1843-1939 | Sentence | denotes | For visualizing aggregate scATAC-seq data, the binarized matrix above was summed and normalized. |
| T445 | 1940-2049 | Sentence | denotes | Scale factors were computed by taking the binarized sum in the global peak set and normalizing to 10,000,000. |
| T446 | 2050-2372 | Sentence | denotes | Tracks were then plotted in Loupe Cell Browser, an interactive visualization software that shows scATAC-seq peak profiles for scATAC-seq cell clusters, similar to the analysis done in this manuscript and described at https://support.10xgenomics.com/single-cellatac/software/visualization/latest/what-is-loupe-cell-browser. |
| T447 | 2374-2382 | Sentence | denotes | chromVAR |
| T448 | 2383-2431 | Sentence | denotes | We measured global TF activity using chromVAR15. |
| T449 | 2432-2613 | Sentence | denotes | We used the cell-by-peaks and the Catalog of Inferred Sequence Binding Preferences (CIS-BP) motif (from chromVAR motifs “human_pwms_v1”) matches within these peaks from motifmatchr. |
| T450 | 2614-2716 | Sentence | denotes | We then computed the GC-bias-corrected deviation scores using the chromVAR “deviationScores” function. |
LitCovid-PD-GlycoEpitope
| Id | Subject | Object | Predicate | Lexical cue | glyco_epitope_db_id |
|---|---|---|---|---|---|
| T1 | 441-444 | GlycoEpitope | denotes | Tn5 | http://www.glycoepitope.jp/epitopes/AN0083 |
| T2 | 859-862 | GlycoEpitope | denotes | Tn5 | http://www.glycoepitope.jp/epitopes/AN0083 |
| T3 | 1621-1624 | GlycoEpitope | denotes | Tn5 | http://www.glycoepitope.jp/epitopes/AN0083 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 1505 | 95-99 | Gene | denotes | hg38 | Gene:8549 |