1. Uncut vector: to check cell competency and antibiotic resistance.
2. Vector cut and not ligated: to check for uncut vector. Gel purification (we recommend Monarch DNA Gel Extraction Kit, NEB #T1020) may be required to remove the last 0.1% of uncut vector.
3. Vector cut and ligated: to check for intact ends and ligation conditions.
4. Vector cut, dephosphoyrlated and ligated: to check for dephosphorylation. Total colony number should be <5% of the vector cut and ligated.