How shall DNA samples be inspected before library preparation?

NadPrep EZ DNA Library Preparation Kitv2 is suitable for various types of samples, including whole blood gDNA, FFPE, etc. For the treatment of complex samples (such as FFPE samples), it is recommended to carry out quality control at the source. If there are impurities such as protein and phenols in DNA samples, the effect of enzymatic digestion may be affected.

• Sample solvent: It is recommended to use nuclease Free Water or 10 mM Tris-HCl (pH 7.5-8.0) to dissolve the DNA samples (the enzymatic fragmentation reagent is sensitive to the concentration of EDTA. Therefore, it is necessary to confirm the concentration of EDTA in the solvent in this step. If the solvent pH is too high, the enzyme activity might be affected, resulting in insufficient fragmentation (1.8X magnetic bead purification can be carried out if necessary).
• Sample quantification: It is recommended to use NanoDrop based on the principle of spectrophotometer as well as Qubit® and PicoGreen® based on double-stranded DNA fluorescent dye for quantitative analysis of general gDNA samples.
• Sample purity: High quality DNA input, with OD260/OD280=1.8-2.0；OD260/OD230=2.0-2.5.
• Sample fragment distribution: It is recommended to use 1% agarose gel electrophoresis for sample size detection or to use bioanalyzer (such as Agilent 2100) DIN value for sample integrity assessment. The samples can be simply classified into four grades as shown in the following figure (the basic four grade classification method; samples can also be further classified according to the actual situation). The enzymatic digestion time of different grades of FFPE samples can be adjusted according to the user manual.

Grading Standard as follows:

A:One clear  strip with about 15 kb in size

B+:One clear and slight trailing strip with about 15 kb in size

B:One indistinct strip with about 15 kb Consistent withg DNA One extra cycle more in size, with medium diffusion

C:Multiple strips ranging from 200 bp to 2,500 bp, with severe diffusion

D:Multiple strips ranging from 100 bp to 1 kp, with severe diffusion