TABLE 3.
Partially purified | qPCR | ddPCR | |||||
downstream sample (number and treatment) | Buffer composition of the sample | Average quantity (vg/mL) | CV% | Bias of DNase to DNase+proteinase K | Average quantity (vg/mL) | CV% | Bias of DNase to DNase+proteinase K |
1 – DNase | 1.5 mM potassium phosphate, pH 8 | 3.8E+11 | 12 | −42% | 8.9E+10 | 3 | −19% |
1 – DNase+Proteinase K | 6.6E+11 | 17 | 1.1E+11 | 4 | |||
2 – DNase | 1.5 mM potassium phosphate, pH 8 | 2.6E+11 | 6 | −54% | 5.5E+10 | 5 | −35% |
2 – DNase+Proteinase K | 5.6E+11 | 11 | 8.5E+10 | 7 | |||
3 – DNase | 1.5 mM potassium phosphate, pH 8 | 1.7E+11 | 20 | −62% | 4.8E+10 | 2 | −27% |
3 – DNase+Proteinase K | 4.5E+11 | 6 | 6.6E+10 | 6∗∗ | |||
4 – DNase | 50 mM acetate, 100 mM NaCl, 0.5% Sucrose, 0.2% Poloxamer, pH 3.7 | 3.5E+10 | 10 | −38% | 6.7E+09 | 2∗∗ | −17% |
4 – DNase+Proteinase K | 5.6E+10 | 7 | 8.1E+09 | 6 | |||
5 – DNase | 50 mM acetate, 100 mM NaCl, 0.5% Sucrose, 0.2% Poloxamer, pH 3.7 | 6.9E+10 | 10 | −37% | 1.5E+10 | 3 | 0% |
5 – DNase+Proteinase K | 1.1E+11 | 8 | 1.5E+10 | 3 | |||
6 – DNase | 20 mM Tris, 2 mM MgCl2, pH 8.0 | 4.4E+10 | 15 | na | 3.4E+10 | 7 | na |
7 – DNase | 1.3 M potassium phosphate pH 7.0 | 3.0E+08* | 42 | na | 4.1E+08 | 8 | na |
8 – DNase | 0.7 M potassium phosphate pH 7.0 | 4.9E+09 | 15 | na | 4.2E+09 | 5 | na |
9 – DNase | 1.5 M potassium phosphate pH 7.0 | 6.3E+09 | 23 | na | 5.8E+09 | 8 | na |
10 – DNase | 1.5 M potassium phosphate pH 7.0 | 3.7E+08* | 30 | na | 2.9E+08 | 12 | na |
11 – DNase | 0.8 M potassium phosphate pH 7.0 | 1.6E+09 | 9 | na | 1.4E+09 | 8 | na |
12 – DNase | 20 mM Tris, 2 mM MgCl2, pH 8.0 | 4.9E+10 | 9 | na | 4.8E+10 | 5 | na |
13 –DNase | 1.1 M potassium phosphate pH 7.0 | 1.5E+10 | 9 | na | 1.2E+10 | 8 | na |
14 – DNase | 1.1 M potassium phosphate pH 7.0 | 1.1E+09* | 27 | na | 1.1E+09 | 12 | na |
Average quantity of the vector genome (vg/mL) was determined from nine to six replicates of qPCR and ddPCR, respectively, unless stated otherwise. *First dilution used in experiment was inhibited (six replicates used for CV% calculation), ∗∗results for only one dilution due to saturated droplets (two replicates used for CV% calculation), na, not applicable.