Table 1.
Summary of single-cell RNA sequencing runs.
| Parameter | 1st 10x run | 2nd 10x run | 3rd 10x run |
|---|---|---|---|
| Cell sorting | DN + γδ | DN1 + DN2 | DN1 & DN2 (55%) γδ (15%) DN3 (30%) |
| Number of cells loaded | 17,500 | 18,000 | 17,500 |
| Targeted number of cells (recovery) | 10,000 | 10,000 | 10,000 |
| Estimated number of cells (From Cell Ranger) |
5,527 | 8,887 | 8,869 |
| Mean Reads per cell | 82,999 | 58,813 | 45,036 |
| Median Genes per cell | 2,149 | 1,814 | 2,735 |
| Median UMI Counts | 5,982 | 4,830 | 8,343 |
| Filtering (no. cells removed) | 5,253 (274) | 8,851 (36) | 7,990 (879) |
| Detecting highly variable genes | 2,036 HVGs (Feature Selection) |
2000 HVGs (VST Selection) |
2000 HVGs (VST Selection) |
| Dimensionality reduction | 15PCs (90% variance) |
11PCs (91% variance) |
11PCs (90% variance) |
| DoubletFinder (PC distance matrix) |
pK = 0.005 | pK = 0.24 | |
| Number of doublets | 700 | 750 | 750 |
| Doublets removal (Dimensionality reduction) |
2,066 HVGs 15PCs (90% variance) |
10PCs (90% variance) |
|
| Resolution (no. clusters) | 2.0 (19) | 2.0 (26) (25- doublets removed) |
2.0 (27) |
| Cell cycle regression (re-clustering) |
14PCs (>90% variance) |
14PCs (>90% variance) |
|
| Cell cycle regression (re-clustering) |
2.0 (19) | 2.0 (25) |