20 DNA only extractions from Porites and Pocillopora Corals from Mo’orea

Using the Zymo Quick-DNA Miniprep Plus kit

Sample Prep

Sample #	Type
40	Massive Porites
41	Pocillopora verrucosa
55	Massive Porites
56	Massive Porites
58	Massive Porites
59	Pocillopora verrucosa
65	Pocillopora verrucosa
67	Massive Porites
75	Massive Porites
159	Pocillopora verrucosa
167	Pocillopora verrucosa
171	Pocillopora verrucosa
208	Massive Porites
220	Massive Porites
222	Massive Porites
232	Pocillopora verrucosa
241	Pocillopora verrucosa
273	Massive Porites
304	Massive Porites
312	Massive Porites

• New Beads were poured into sample tubes. The new beads should be easier to pipette the liquid out of them as the do not get sucked up by the p20
• Samples were homogenized by vortexing for ~60 seconds for all samples
• Most of the liquid from the tubes was removed by pipetting. This was about 400µl. The tubes contained a small amount of liquid and un-homogenized tissue left, so 200µl of DNA/RNA shield was added to each tube and those were put back into the -20
• Following recommendations for samples in DNA/RNA Shield from the kit protocol, 200µl of Solid Tissue Buffer and 12µl of Proteinase K were added to each sample
• Samples were votexed, spun down, and incubated at 55 degrees C for 5 hours shaking at 600rpm

Following DNA extraction went along exactly as previous post

Qubit

• Broad Range dsDNA Qubit protocol
• Qubit standards and master mix working stock was made by Kevin Wong
• All samples were read twice

Sample	DNA Standard 1 (RFU)	DNA Standard 2 (RFU)	DNA 1 (ng/µl)	DNA 2 (ng/µl)	Average DNA
40	209	23359	26.6	26.4	26.5
41	209	23359	88.8	88.2	88.5
55	209	23359	29.8	29.6	29.7
56	209	23359	21.6	21.4	21.5
58	209	23359	8.42	8.34	8.38
59	209	23359	30.4	30.2	30.3
65	209	23359	56.4	56	56.2
67	209	23359	4.9	4.8	4.85
75	209	23359	35	34.8	34.9
159	209	23359	54.2	53.8	54
167	209	23359	64.2	63.8	64
171	209	23359	60	60	60
208	209	23359	14.8	14.6	14.7
220	209	23359	15.8	15.6	15.7
222	209	23359	41	40.6	40.8
232	209	23359	74.2	73.8	74
241	209	23359	44	43.8	43.9
273	209	23359	9.22	9.14	9.8
304	209	23359	54.2	53.8	54
312	209	23359	29.4	29.2	29.5

67 and 220 were re-dos, so there might not have been that much left in the first place. I need to do a gel to see how the quality is.

Gel Verification

• A 1.5% agarose gel was ran to check the integrity of the genomic DNA
• Following the PPP Lab protocol
• Samples 67 and 220 were not run on the gel