Table 4 Variable parameters applied to chromatin from different starting cell numbers
From: Limitations and possibilities of low cell number ChIP-seq
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 |