From: Limitations and possibilities of low cell number ChIP-seq
Protocol & cell number / ChIP | Bench’ | New | New | New | New | New |
---|---|---|---|---|---|---|
2 x 107 | 2 x 107 | 2.5 x 106 | 5 x 105 | 1 x 105 | 2 x 104 | |
Total number reads | 13 402 262 | 13 798 839 | 14 136 243 | 16 693 519 | 15 601 563 | 56 904 707 |
Number unique, non-duplicate reads | 6 011 891 | 7 0330 709 | 5 794 519 | 3 463 886 | 2 423 126 | 661 591 |
Number of peaks called (fraction relative to benchmark) | 16 545 | 16 244 | 17 054 | 15 636 | 14 771 | 12 296 |
(1) | (0.98) | (1.03) | (0.95) | (0.89) | (0.74) | |
Sensitivity relative to benchmark | 1 | 0.93 | 0.96 | 0.89 | 0.85 | 0.69 |
Specificity relative to benchmark | 1 | 0.94 | 0.93 | 0.95 | 0.97 | 0.98 |