PMC:7039956 / 17034-17914
Annnotations
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 413 | 868-874 | Chemical | denotes | Seurat |
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T313 | 7-11 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T314 | 12-15 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T315 | 91-95 | Body_part | denotes | Cell | http://purl.org/sig/ont/fma/fma68646 |
| T316 | 196-200 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T317 | 224-231 | Body_part | denotes | tissues | http://purl.org/sig/ont/fma/fma9637 |
| T318 | 264-269 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T319 | 325-330 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T320 | 408-413 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T321 | 621-628 | Body_part | denotes | tissues | http://purl.org/sig/ont/fma/fma9637 |
| T322 | 744-749 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T323 | 751-755 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T322 | 7-11 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T323 | 91-95 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | Cell |
| T324 | 196-200 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T325 | 264-269 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T326 | 280-285 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
| T327 | 325-330 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T328 | 387-392 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
| T329 | 408-413 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T330 | 603-610 | http://purl.obolibrary.org/obo/BFO_0000030 | denotes | objects |
| T331 | 744-749 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T332 | 751-761 | http://purl.obolibrary.org/obo/CL_0000000 | denotes | cell types |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T108 | 0-51 | Sentence | denotes | Single cell RNA-seq data preprocessing and analysis |
| T109 | 52-146 | Sentence | denotes | The FASTQ files were analyzed with the Cell Ranger Software Suite (version 3.1; 10× Genomics). |
| T110 | 147-232 | Sentence | denotes | The Seurat (version 3.0) was applied to read the gene-barcode matrix of four tissues. |
| T111 | 233-373 | 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 | 374-432 | Sentence | denotes | Besides, the genes detected in <3 cells were filtered out. |
| T113 | 433-629 | 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 | 630-809 | 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 | 810-880 | Sentence | denotes | UMAP plots, heatmap, and violin plots were generated with Seurat in R. |