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Discouraging - no DNA in the pooled samples that should have DNA. There is low-level DNA in the ligated samples - actually less than after the double digestion.
Potential problems:
Though I couldn’t find anything specific about percent DNA recovery following AMPure bead purification on Beckman Coulter’s website, this awesome lab page gave results showing about 70% recovery with 1.4 - 1.6 bead ratio. Seems okay.
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