TITLE: Salting-out Protocol for Extracting HMW Genomic DNA from frozen octocorals
AUTHORS: Santiago Herrera

[DESCRIPTION]
Salting-out protocol for extracting high-molecular weight (HMW) genomic DNA from frozen octocorals for genomic methods. Suitable for genome sequencing, RAD-seq and other methods that require HMW DNA. Starting material must be alive when flash-frozen in liquid nitrogen and always stored below -80C.

[GUIDELINES]
Follow steps 1-12

[STEPS]
SECTION: Preparation
1. Make sure that there are enough Materials and Supplies available and at the right temperature conditions.
SECTION: Preparation
2. Make sure that the Ultracentrifuge, Heat Block and IncuShaker are set up in the fume hood.
SECTION: Preparation
3. Place tube rack in IncuShaker.
SECTION: Preparation
4. Turn on the Heat Block and the IncuShaker and set to 65°C.
SECTION: Preparation
5. Pre-label 3 sets of 1.5ml microcentrifuge tubes for each sample (label one of the three tubes [the last one to be used] with a green tough-spot and full SH ID in addition to labelling the side of the tube with the date of the extraction.
SECTION: Preparation
6. Prepare the following digestion mix for each tube (mix in a 2.0ml tube, scale accordingly for up to 4 samples) and pre-heat in hot plate:  350µl cell lysis buffer,  42µl 0.5 M EDTA. 
SECTION: Preparation
7. Fill 3L Stainless Steel Dewar Flask with liquid N2
SECTION: Preparation
8. Fill a small Styrofoam cooler with dry ice
SECTION: Preparation
9. Fill a small Styrofoam cooler with crushed ice
SECTION: Preparation
10. 10.   Take cryovials containing frozen tissues out of -80C freezer and place in styrofoam cooler with dry ice.
SECTION: Preparation
11. 11.   Take Proteinase K, 7.5M ammonium acetate, 100% isopropanol, and 70% ethanol stocks out of fridge and place in cooler with crushed ice.
12. 12.   Pour liquid N2 from the Stainless Steel Dewar Flask into the Liquid Nitrogen Cooled Mini Mortar base up to the fill line and then place the metal microcentrifuge tube mortar holder in the base to chill.  Digestion
SECTION: Digestion
13. 13.   Sterilize the small forceps and the metal Pestle by exposing to the flame of the alcohol burner for ~10 seconds. Cool each tool by squirting distilled water on the tools (place collection beaker below to catch the water). Dry up the tools by shaking them vigorously.
SECTION: Digestion
14. 14.   Place forceps on top of a clean piece of aluminium foil.
SECTION: Digestion
15. 15.   Place the tip of the metal Pestle in a new Whirl-Pak bag
SECTION: Digestion
16. 16.   Place a 1.5 mL microcentrifuge tube (corresponding to the right sample) in the chilled MiniMortar.
SECTION: Digestion
17. 17.   Break a small piece of coral tissue (~3mm3) with the forceps (it should be very brittle and easy to break) and place in the microcentrifuge tube that is sitting in the MiniMortar.
SECTION: Digestion
18. 18.   Wipe forceps with clean Kim-wipe and place on the Aluminium foil.
SECTION: Digestion
19. 19.   Chill the Pestle by immersing the tip in liquid N2 (~10s in the Dewar Flask) while keeping it in the Whirl-pak bag.
SECTION: Digestion
20. 20.   Grind the sample to a powder with the Pestle until you don’t feel any more crunching.
SECTION: Digestion
21. 21.   Wipe Pestle with clean Kim-wipe and place on Aluminium foil.
SECTION: Digestion
22. 22.   Loosen pulverized tissue by quickly flicking the bottom end of the tube with your finger.
SECTION: Digestion
23. 23.   Add pre-heated 392µl of digestion mix and quickly mix by inverting and flicking. Place tube in heat block.
SECTION: Digestion
24. 24.   Add 10µl of Proteinase K to the mix. Place in tube rack in IncuShaker (minimize door opening).
SECTION: Digestion
25. 25.   Repeat steps 13-24 for each sample.
SECTION: Digestion
26. 26.   Incubate at 65oC for 2.5-3 hours. Mix digestion rack by invesion every 20-30min
SECTION: Digestion
27. 27.   Optional Add 2 µl RNase A.  Mix by vortexing.  Incubate at 37oC for 30 minutes.        Protein and Cellular Debris Precipitation
SECTION: Protein and Cellular Debris Precipitation
28. 28.   Add 140 µl 7.5 M ammonium acetate to each tube.  Mix by inversion.  Incubate at 4oC (in the fridge) for 10 minutes.
SECTION: Protein and Cellular Debris Precipitation
29. 29.   Centrifuge at 12,000xg for 10 minutes.
SECTION: Protein and Cellular Debris Precipitation
30. 30.   Transfer supernatant (500 µl) to a new 1.5 ml microcentrifuge tube. Be careful not to disturb waste pellet.
SECTION: Protein and Cellular Debris Precipitation
31. 31.   Repeat steps 28-29.
SECTION: Protein and Cellular Debris Precipitation
32. 32.   Transfer supernatant to a new 1.5 ml microcentrifuge tube (with the green tough spot label). Be careful not to disturb waste pellet.
SECTION: DNA Precipitation
33. 33.   Add 680 µl cold isopropanol (volume ratio ~1:1).  Mix by inverting gently ~50 times. Centrifuge at 8000 xg for 5 minutes.
SECTION: DNA Precipitation
34. 34.   Carefully discard the supernatant, by pouring out. Keep an eye on DNA pellet to avoid avoiding loosing it.
SECTION: DNA Precipitation
35. 35.   Pulse centrifuge the tubes and pipette out remaining supernatant while avoiding contact with the DNA pellet.  DNA Washing
SECTION: DNA Washing
36. 36.   Add 800 µl 70 % ethanol.  Invert the tube several times to wash the DNA pellet. Centrifuge at 8000 xg for 1 minute.
SECTION: DNA Washing
37. 37.   Carefully discard the supernatant, by pouring out. Keep an eye on DNA pellet to avoid avoiding loosing it.
SECTION: DNA Washing
38. 38.   Repeat steps 36-37.
SECTION: DNA Washing
39. 39.   Pulse centrifuge the tubes and pipette out remaining ethanol while avoiding contact with the DNA pellet.
SECTION: DNA Washing
40. 40.   Allow pellet to air dry for 20 minutes.  Avoid over-drying the DNA pellet, as the DNA will be difficult to dissolve.  DNA Rehydration
SECTION: DNA Rehydration
41. 41.   Re-suspend dried pellets with 150 µl TE or AE buffer.  Invert tube to mix and spin down using a centrifuge.
SECTION: DNA Rehydration
42. 42.   Incubate at room temperature for 60 minutes or incubate in the fridge overnight.
SECTION: DNA Rehydration
43. 43.   Pulse centrifuge the tubes and store at -20oC.