1. Place 1/4 seed into each well of a 96-round well deep well plate.
2. Add 400ul SDS extraction buffer (200 mM Tris-HCl pH 7.5, 250 mM NaCl, 25 mM EDTA, 0.5% SDS) to each well. Add 5ul Proteinase K (4mg/ml final concentration 50ug/ml) to each well, gently vortex to mix and spin down. Place in a 65 °C incubator for 2 hours, shaking at 225 rpm.
3. Add 260ul 5 M NaCl to each well, vortex gently to mix, and incubate at 4°C for 20'. Centrifuge for 15' at 3600 rpm.
4. Add 150ul isopropanol (2/3 volume) into a new 96 round well deep well plate.
5. Aspirate off 200ul supernatant and add to the isopropanol plate. Vortex to mix. Allow to sit >15' at -20°C. Store the seed block at -20°C in case samples need to be re-extracted.
6. Centrifuge for 15' at 3600 rpm. Carefully decant isopropanol (handle gently, pellets can be slippery).
7. Add 400ul 70% ethanol. Centrifuge 15' at 3600 rpm. (If necessary, the extraction can be paused at this stage. Store plates at 4°C until resuming.)
8. Carefully decant ethanol. Invert plate for no longer than 2 seconds, as pellets can be slippery. Centrifuge at 1500 rpm to assure that pellets are at bottom of plate.
9. Allow the plate to sit for 60' at 65°C in shaker/incubator until residual alcohol has completely evaporated. Using high heat for this step seems to help remove proteins and other debris that can inhibit PCR.
10. Resuspend the dried pellet in 100ul water for 60' at 37°C in shaker/incubator, or store at 4°C overnight. Transfer samples to a new 96-well PCR plate and centrifuge at 3600 rpm for 5'. Quantitate a few samples to estimate DNA concentration (concentration will usually be ~100ng/ul; the 260/280 ratio around 1.9; and the 260/230 ratio around 1.3. The 230/260 ratio is used to determine the level of residual carbohydrates). Make a 5x dilution of the supernatant for your PCR template (avoid aspirating the pellet) for use on the Roche LC480 light cycler .

Reference
Edwards, et al. Nucleic Acids Research 19(6): 1349.