Some important points include:
Remove as much paraffin as possible around the sample before beginning.
If you have a tissue with a small surface area, you can consider reducing the amount of Lysis Buffer (minimum of 70μl). Please see this FAQ for more information.
Check that the sample is well submerged in the Lysis Buffer.
The Removal Solution is light sensitive and provided in a brown bottle. Take care when storing/using this reagent.
Ensure Spin Column is prepared appropriately. Please vortex well and spin down prior to removing Storage Buffer, and ensure no air bubbles are present. Refer to this FAQ for additional tips on column preparation.
Prior to DNase digestion, check for the absence of paraffin in the aqueous phase when letting the sample cool down. If you observe a jelly layer on top of the aqueous phase, this means that you have some paraffin in your sample. Reheat the sample and centrifuge again. Take out the aqueous phase.
Increase the centrifugation speed to maximize the phase separation.
When centrifuging the final eluate, do not increase the speed. If >1,000 × g is used, this can lead to impurities in your final sample.