One explanation is that the supernatant is below the pellet because the centrifugation speed or time was too high or too long, which caused the DNA to be sheared and fragmented, and to sediment at the bottom of the tube. To avoid this, you should use a lower centrifugation speed or time, or use a gentle pipetting or vortexing to resuspend the pellet1.

Another explanation is that the supernatant is below the pellet because the STE buffer was not prepared correctly, which affected the solubility and stability of the DNA. To avoid this, you should make sure that the STE buffer has the correct pH, concentration, and temperature, and that it is sterile and free of contaminants. You should also check the expiration date of the buffer components and store them properly23.

A third explanation is that the supernatant is below the pellet because the sample was contaminated with proteins, lipids, or polysaccharides, which formed a viscous layer at the bottom of the tube and trapped the DNA. To avoid this, you should use a proper lysis method to break down the cell membranes and release the DNA, and use a proteinase K or RNase A treatment to digest the proteins or RNA. You should also use a phenol-chloroform extraction or an ethanol precipitation to remove the impurities45.