Soft and Hard Homogenization DNA/RNA Extractions #91-118

20190724 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.

Extractions #91-98 done together and extractions #99-118 done together.
Extractions #91-98 start 9:15 end 12:05
Extractions #99-118 start 12:15 end 16:36

Timepoint	Species	Coral ID	Extraction ID	Homogenization
20181117	Montipora	1332	91	soft
20181117	Montipora	1332	92	hard
20181117	Montipora	1074	93	soft
20181117	Montipora	1074	94	hard
20181103	Montipora	1420	95	soft
20181103	Montipora	1420	96	hard
20181215	Montipora	1555	97	soft
20181215	Montipora	1555	98	hard
20181103	Montipora	1148	99	soft
20181103	Montipora	1148	100	hard
20181103	Pocillopora	2202	101	soft
20181103	Pocillopora	2202	102	hard
20181103	Pocillopora	2305	103	soft
20181103	Pocillopora	2305	104	hard
20181103	Montipora	2862	105	soft
20181103	Montipora	2862	106	hard
20181020	Montipora	1260	107	soft
20181020	Montipora	1260	108	hard
20180922	Montipora	2561	109	soft
20180922	Montipora	2561	110	hard
20181117	Pocillopora	1732	111	soft
20181117	Pocillopora	1732	112	hard
20180922	Pocillopora	2743	113	soft
20180922	Pocillopora	2743	114	hard
20180922	Pocillopora	1219	115	soft
20180922	Pocillopora	1219	116	hard
20181117	Pocillopora	2550	117	soft
20181117	Pocillopora	2550	118	hard

Fragments #1074, #1732, and #2202 were paler in color and liquid looked less dense after soft and hard homogenizations.

Qubit Results:

DNA (ng/μl)
Standard 1	215.12
Standard 2	23344.97
Coral ID	Extraction ID	Reading
1332	91	35
1332	92	24
1074	93	41.2
1074	94	22.2
1420	95	49.8
1420	96	32.8
1555	97	51.4
1555	98	31.4

DNA (ng/μl)
Standard 1	226.84
Standard 2	24638.56
Coral ID	Extraction ID	Reading
1148	99	59.2
1148	100	28
2202	101	70.8
2202	102	50.8
2305	103	80.8
2305	104	83
2862	105	30.2
2862	106	24
1260	107	19.6
1260	108	11.9
2561	109	14.8
2561	110	16.9
1732	111	46.2
1732	112	42.6
2743	113	106
2743	114	101
1219	115	77.4
1219	116	40.2
2550	117	38.6
2550	118	60.4

RNA (ng/μl)
Standard 1	413.78
Standard 2	11048.94
Coral ID	Extraction ID	Reading
1332	91	31.2
1332	92	17.8
1074	93	14.8
1074	94	10.4
1420	95	30.2
1420	96	19.2
1555	97	31.2
1555	98	20.8

RNA (ng/μl)
Standard 1	408.66
Standard 2	11009.82
Coral ID	Extraction ID	Reading 1	Reading 2	Average
1148	99	26.4	25.8	26.1
1148	100	15	15	15
2202	101	77.4	77.4	77.4
2202	102	50.8	50.8	50.8
2305	103	94.6	94.4	94.5
2305	104	63.2	63.2	63.2
2862	105	21	20.8	20.9
2862	106	14.2	14.2	14.2
1260	107	16.8	16.8	16.8
1260	108	11.2	11	11.1
2561	109	16.6	16.8	16.7
2561	110	12.4	12	12.2
1732	111	54.6	54.6	54.6
1732	112	37.2	37.2	37.2
2743	113	103	103	103
2743	114	69	69	69
1219	115	75.8	75.6	75.7
1219	116	53.2	52.8	53
2550	117	47	47	47
2550	118	42.8	42.8	42.8

Two readings were only done for RNA extractions #99-118.

Gel Electrophoresis Results:

Extractions #91-98

Extractions #99-111

Extractions #112-118

TapeStation Results:

Coral ID	Extraction ID	RIN
1332	91	7
1332	92	7.3
1074	93	8.2
1074	94	**
1420	95	8.2
1420	96	8.3
1555	97	8.4
1555	98	8.2
1148	99	8.5
1148	100	8.5
2202	101	8.2
2202	102	7.6
2305	103	7.7
2305	104	7.7
2862	105	8.8
2862	106	8.9
1260	107	8.8
1260	108	8.1
2561	109	8
2561	110	8.2
1732	111	8.4
1732	112	8.1
2743	113	7
2743	114	6.5
1219	115	7.4
1219	116	7.4
2550	117	8.6
2550	118	8.3

TapeStation report #1 does not have descriptions. Order of samples: Ladder, 91-98.
Link to 20190724 report #1, Extractions #91-98
Link to 20190724 report #2, Extractions #99-118