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.

Gilfillan et al. BMC Genomics 2012 13:645   doi:10.1186/1471-2164-13-645

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