Tubes need to be pooled after breaking the emulsions following Targeted PCR. Follow the protocol to break the emulsions, increasing the aqueous layer with added nuclease free water.
V2 Chemistry
Pool 42 μL from each aqueous phase to two new 1.5 mL DNA low-bind Eppendorf tubes. Pool contents from tubes 1-4 and 5-8.
V3 Chemistry
Pool 42 μL from each aqueous phase to one new 1.5 mL DNA low-bind Eppendorf tubes, pooling contents from all eight tubes.