Soft and Hard Homogenization DNA/RNA Extractions #73-82

20190722 and 20190723 E.S. DNA/RNA Extractions from Montipora capitata and Pocillopora acuta adult coral fragments from Holobiont Integration Hawaii 2018 project.

Soft and Hard homogenization, and DNA/RNA Extractions followed this protocol. General Zymo Duet DNA/RNA Extraction protocol found here.
Coral fragments were randomly chosen from different timepoint bags.

Timepoint	Species	Coral ID	Extraction ID	Homgenization
20181215	Montipora	1555	73	soft
20181215	Montipora	1555	74	hard
20181117	Montipora	1074	75	soft
20181117	Montipora	1074	76	hard
20181117	Montipora	1095	77	soft
20181117	Montipora	1095	78	hard
20180922	Montipora	1751	79	soft
20180922	Montipora	1751	80	hard
20181020	Pocillopora	2304	81	soft
20181020	Pocillopora	2304	82	hard

Fragment prep start 15:05 end 15:22
Soft/Hard homogenization start 15:23 end 15:48
Extractions start 15:49 end 17:53

50 μl of 100% ethanol added to extraction #s: 79, 73, 75, 82, and 81 in final elution step accidentally. Final volume of the above 5 DNA extractions is 150 μl. Residual ethanol will prevent full hydration and elution of nucleic acids, and too much ethanol will cause the sample to not sink into a well in the DNA gel. These five samples might be too diluted to quantify DNA.

Qubit Results:

DNA (ng/μl)
Standard 1	209.93
Standard 2	23170.52
Coral ID	Extraction ID	Reading 1	Reading 2	Average
1555	73	4.58	4.54	4.56
1555	74	7.72	7.7	7.71
1074	75	**	**	**
DNA
Standard 1	169.27
Standard 2	18543.03
Coral ID	Extraction ID	Reading 1	Reading 2	Average
1074	76	5.38	5.28	5.33
1095	77	7.54	7.44	7.49
1095	78	8.32	8.28	8.3
1751	79	2.9	2.88	2.89
1751	80	8	7.96	7.98
2304	81	25.2	25	25.1
2304	82	12.8	12.7	12.75

RNA (ng/μl)
Standard 1	411.38
Standard 2	12375.27
Coral ID	Extraction ID	Reading 1	Reading 2	Average
1555	73	**	**	**
1555	74	**	**	**
1074	75	**	**	**
1074	76	**	**	**
1095	77	**	**	**
1095	78	**	**	**
1751	79	**	**	**
1751	80	**	**	**
2304	81	24.4	24.4	24.4
2304	82	32.2	32.4	32.3

Gel Electrophoresis Results:

Because of the ethanol added to 5 of the DNA samples, 3 of the samples did not sink into the gel - #73, 75, and 82.

TapeStation Results:

Coral Fragment ID	Extraction ID	RIN
1555	73	**
1555	74	**
1074	75	**
1074	76	**
1095	77	**
1095	78	**
1751	79	**
1751	80	**
2304	81	9
2304	82	8.7

Link to 20190723 report #3, Extractions #68-82

Will re-do fragment #s: 1420, 1689, 1235, 1332, 1555, 1074, 1095, and 1751.