Limitations and possibilities of low cell number ChIP-seq

BMC Genomics

Table 1 Peak calling, sensitivity (detection of peaks called in the benchmark) and specificity (off-target peaks not present in the benchmark)

Protocol & cell number / ChIP	Bench’	New	New	New	New	New
Protocol & cell number / ChIP	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
Number of peaks called (fraction relative to benchmark)	(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

Peaks were called using MACS, allowing no ambiguously mapping or duplicate reads.

ISSN: 1471-2164