From: Protein velocity and acceleration from single-cell multiomics experiments
Dataset | CITE-seq | REAP-seq | ECCITE-seq ctrl | ECCITE-seq CTCL | 10X 1k | 10X 10k |
---|---|---|---|---|---|---|
RNA data | GSM2695381 | GSM2685238 | GSM3596095 | GSM3596100 | See Methods | See Methods |
Protein data | GSM2695382 | GSM2685243 | GSM3596096 | GSM3596101 | See Methods | See Methods |
Alignment software | Cell Ranger 2.2 | Cell Ranger 1.3 | Cell Ranger 3.0 | Cell Ranger 3.0 | kallisto 0.46 | kallisto 0.46 |
Counting software | velocyto 0.17 | velocyto 0.17 | velocyto 0.17 | velocyto 0.17 | kallisto 0.46 | kallisto 0.46 |
Reference genome | GRCh38 | hg19 | hg19 | hg19 | GRCh38 | GRCh38 |
Cell count | 1780 | 3158 | 5084 | 5317 | 709 | 7855 |
Velocity genes | 1172 | 1338 | 591 | 667 | 1114 | 920 |
Antibodies | 10 | 41 | 49 | 49 | 17 | 17 |
Velocity proteins | 7 | 16 | 11 | 12 | 7 | 8 |
Cell types found | 5 | 4 | 4 | 3 | 5 | 5 |
Imputation k | 400 | 800 | 800 | 800 | 50 | 50 |
Clustering method | MVP | RVP | RVP | MVP | MVP | MVP |
Embedding | PC2/3 and t-SNE | t-SNE | t-SNE | t-SNE | t-SNE | t-SNE |