Table 4 |
||||||
| Variable parameters applied to chromatin from different starting cell numbers | ||||||
| Protocol & starting cell number | Benchmark | New | New | New | New | New |
| 4 x 107 | 4 x 107 | 5 x 106 | 1 x 106 | 2 x 105 | 4 x 104 | |
| Cells per IP | 2 x 107 | 2 x 107 | 2.5 x 106 | 5 x 105 | 1 x 105 | 2 x 104 |
| MNase digestion volume (cells / ml) | 1500 μl | 1500 μl | 500 μl | 100 μl | 20 μl | 20 μl |
| (2.7 x 107/ml) | (2.7 x 107/ml) | (1 x 107 / ml) | (1 x 107 / ml) | (1 x 107 / ml) | (2 x 106 / ml) | |
| IP volume | 750 μl | 1500 μl | 500 μl | 100 μl | 100 μl | 100 μl |
| (in 1.5 ml tube) | (in 2 ml tube) | (in 1.5 ml tube) | (in 0.2 ml PCR tube) | (in 0.2 ml PCR tube) | (in 0.2 ml PCR tube) | |
| Protein A/G bead volume for preclearing / IP | 50 μl | 50 μl | 50 μl | 10 μl | 10 μl | 10 μl |
| Antibody amount / IP | 5μg | 5μg | 5μg | 1 μg | 1 μg | 1 μg |
| Wash buffer volumes | 1 ml | 1 ml | 1 ml | 150 μl | 150 μl | 150 μl |
“Benchmark” refers to the protocol now published by Zhao and colleagues [21] and “new” to the method presented here.
Gilfillan et al. BMC Genomics 2012 13:645 doi:10.1186/1471-2164-13-645
