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Why am I not getting enough DNA from the labeling reaction?

OBSERVATION(S) POTENTIAL CAUSE OPTIONS TO RESOLVE
Low DNA recovery from membrane as determined by post-stain Qubit HS quantitation DNA is too viscous to fully remove from membrane using the recommended pipette setting in the protocol Set the pipette to 50 μl (or up to 100 μl) and move the tip back and forth across the membrane to ensure all DNA is removed
DNA is non-homogenous before beginning DLS Perform additional mixing of the DNA with a wide-bore pipette tip (5x up and down). Allow DNA to homogenize at room temperature overnight. Repeat quantitation with the Qubit BR assay and then repeat DLS if the concentration is within 36 – 150 ng/μl with CV < 0.3

Why are my N50s low?

OBSERVATION(S) POTENTIAL CAUSE OPTIONS TO RESOLVE
Average N50 ≥ 150kbp is < 230 kbp Nuclease contamination Ensure that only nuclease-free water is used for all protocol steps.
Note: water provided in Bionano Kits is nuclease-free.
Freeze-thaw cycles Take care to avoid any additional freeze-thaw cycles of starting sample.

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