Here are a few tips that I have picked up along the way to get the most out of your DNA extraction kits:
(1) If you plan on needing a lot of DNA, you can use the same spin column for multiple extractions from the same sample (Qiagen will not sell spin columns separately). When I was screening microsatellites and needed a lot of DNA, I used the same spin column 5 times to extract DNA out of both blood and tissue samples without a decrease in the quality of the DNA. Just don't mix up the spin columns since they likely still contain DNA on the spin column membrane from the previous extraction! Since I discovered this, I routinely do two rounds of extractions (400µL DNA total) from all samples that allow it (e.g. everything except molted feathers, some predated eggs, and some plucked feather samples where there are only a few feathers). This saves time and money.
(2) You can buy various solutions from Qiagen if you run out - Buffer AL, Proteinase K, and Buffer ATL. For the eggshell membrane extractions, you go through a lot of Buffer ATL, Buffer AL, and Proteinase K since you have to increase the volumes.
(3) Don't skimp on the starting amount of your sample. If you have 5 plucked feathers from a bird, use them all in a single extraction and get 200µL of DNA instead of trying to do several extractions with 2 and 3 feathers. If you use all 5 to start with, you seem to get better quality DNA.
(4) When using the QIAamp® DNA Micro Kit, take your spin columns out of the fridge the day before you plan on doing your extractions. If you try to use them cold, your DNA quality is way lower than if you use them warm.
(5) If you aren't going to use your Proteinase K within 6 months of purchasing the kit, freeze it at -20˚C. The other reagents seem to keep for several years with no problems.
(6) Keep the Buffer AL in a box or somewhere that it is not exposed to light!!!
(7) Use cold 100% Ethanol (kept at -20˚C) for your DNA precipitation step. Warm 100% Ethanol (room temperature) works, but yields slightly lower DNA concentrations.
(8) Always elute your DNA at 6000-7000 X g or the caps off of your 1.5mL microcentrifuge tubes will rip off in the centrifuge
(9) For mouth swab DNA extractions, put the Q-Tip™ in a 2.0mL microcentrifuge tube and not a 1.5mL microcentrifuge tube. If you use a 1.5mL microcentrifuge tube, you will have to transfer it to a 2.0 mL microcentrifuge tube due to the increased Buffer volumes used and the size of the Q-Tip™