Table 1.
Single-cell sequencing reveals widespread on-target proximal deletions from CRISPR–Cas9
| Perturbation type | Dataset | Cell type | Total number of tested targets | Tested loss direction | Number of targets with specific loss | Number of targets with loss toward telomere | Number of targets with loss toward centromere |
|---|---|---|---|---|---|---|---|
| CRISPR–Cas9 | Papalexi | THP-1 (monocytic leukemia) | 24 | 3′ | 6 (25.0%) | 5 (20.8%) | 1 (4.2%) |
| 5′ | 1 (4.2%) | 1 (4.2%) | 0 (0.0%) | ||||
| Frangieh | Melanocytes (melanoma) | 237 | 3′ | 31 (13.1%) | 23 (9.7%) | 8 (3.4%) | |
| 5′ | 34 (14.3%) | 20 (8.4%) | 14 (5.9%) | ||||
| CRISPRi | Replogle | RPE1 | 2,066 | 3′ | 45 (2.2%) | 31 (1.5%) | 14 (0.7%) |
| 5′ | 45 (2.2%) | 11 (0.5%) | 34 (1.6%) | ||||
| Tian | Induced pluripotent stem cell-derived neurons | 177 | 3′ | 3 (1.7%) | 3 (1.7%) | 0 (0.0%) | |
| 5′ | 4 (2.3%) | 2 (1.1%) | 2 (1.1%) | ||||
| Adamson | K562 (leukemia) | 78 | 3′ | 1 (1.3%) | 1 (1.3%) | 0 (0.0%) | |
| 5′ | 2 (2.6%) | 1 (1.3%) | 1 (1.3%) |
The number and percent of target genes showing deletions specific to the target region in two CRISPR–Cas9 and three CRISPRi datasets uniformly reprocessed in scPerturb.