PMC:7039956 / 17086-17914
Annnotations
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 413 | 816-822 | Chemical | denotes | Seurat |
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T315 | 39-43 | Body_part | denotes | Cell | http://purl.org/sig/ont/fma/fma68646 |
| T316 | 144-148 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T317 | 172-179 | Body_part | denotes | tissues | http://purl.org/sig/ont/fma/fma9637 |
| T318 | 212-217 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T319 | 273-278 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T320 | 356-361 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T321 | 569-576 | Body_part | denotes | tissues | http://purl.org/sig/ont/fma/fma9637 |
| T322 | 692-697 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T323 | 699-703 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T323 | 39-43 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | Cell |
| T324 | 144-148 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T325 | 212-217 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T326 | 228-233 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
| T327 | 273-278 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T328 | 335-340 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
| T329 | 356-361 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T330 | 551-558 | http://purl.obolibrary.org/obo/BFO_0000030 | denotes | objects |
| T331 | 692-697 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T332 | 699-709 | http://purl.obolibrary.org/obo/CL_0000000 | denotes | cell types |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T109 | 0-94 | Sentence | denotes | The FASTQ files were analyzed with the Cell Ranger Software Suite (version 3.1; 10× Genomics). |
| T110 | 95-180 | Sentence | denotes | The Seurat (version 3.0) was applied to read the gene-barcode matrix of four tissues. |
| T111 | 181-321 | Sentence | denotes | To control quality, we removed cells with <200 genes and 500 UMI counts, and as well as the cells with mitochondrial content higher than 5%. |
| T112 | 322-380 | Sentence | denotes | Besides, the genes detected in <3 cells were filtered out. |
| T113 | 381-577 | Sentence | denotes | The “sctransform” wrapper in Seurat was applied to normalize the data and remove confounding sources of variation, the “IntegrateData” was used for integrated the Seurat objects from four tissues. |
| T114 | 578-757 | Sentence | denotes | The uniform manifold approximation and projection (UMAP) was used for dimensionality reduction and clustering the cells, cell types were assigned based on their canonical markers. |
| T115 | 758-828 | Sentence | denotes | UMAP plots, heatmap, and violin plots were generated with Seurat in R. |