Soft and Hard Homogenization DNA/RNA Extractions #33-52

20190720 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	Homogenization
20180922	Pocillopora	2363	33	Soft
20180922	Pocillopora	2363	34	Hard
20181103	Pocillopora	1486	35	Soft
20181103	Pocillopora	1486	36	Hard
20181117	Pocillopora	1159	37	Soft
20181117	Pocillopora	1159	38	Hard
20181117	Pocillopora	1641	39	Soft
20181117	Pocillopora	1641	40	Hard
20181117	Montipora	2554	41	Soft
20181117	Montipora	2554	42	Hard
20181103	Pocillopora	1594	43	Soft
20181103	Pocillopora	1594	44	Hard
20181117	Pocillopora	1205	45	Soft
20181117	Pocillopora	1205	46	Hard
20180922	Montipora	2731	47	Soft
20180922	Montipora	2731	48	Hard
20181103	Pocillopora	1451	49	Soft
20181103	Pocillopora	1451	50	Hard
20180922	Pocillopora	1418	51	Soft
20180922	Pocillopora	1418	52	Hard

Fragment Preparation start 9:08 end 9:46
Soft/Hard homogenizations start 9:46 end 10:31
Extractions start 10:31 end 13:35
~4.5 hours for 10 coral fragments (20 DNA, 20 RNA Extractions)

Qubit Results:

DNA (ng/μl)
Standard 1	181.64
Standard 2	21322.7
Coral ID	Extraction ID	Reading 1	Reading 2	Average
2363	33	57.2	57.2	57.2
2363	34	40.4	40	40.2
1486	35	43	42.8	42.9
1486	36	37.2	37.2	37.2
1159	37	53.2	53	53.1
1159	38	4.4	4.36	4.38
1641	39	34.6	34	34.3
1641	40	27	26.8	26.9
2554	41	58.4	58.2	58.3
2554	42	31.2	31.2	31.2
1594	43	28.2	28	28.1
1594	44	16.1	16.1	16.1
1205	45	34.6	34.6	34.6
1205	46	27.4	27.2	27.3
2731	47	27.4	27.4	27.4
2731	48	12.9	12.8	12.85
1451	49	39.4	39.2	39.3
1451	50	39.6	39.4	39.5
1418	51	32	31.8	31.9
1418	52	31.2	31.2	31.2

RNA (ng/μl)
Standard 1	397.95
Standard 2	10082.2
Coral ID	Extraction ID	Reading 1	Reading 2	Average
2363	33	69.4	69.4	69.4
2363	34	48	48	48
1486	35	82.6	82.6	82.6
1486	36	48.2	48	48.1
1159	37	47	47	47
1159	38	45.2	45.2	45.2
1641	39	46.4	46.4	46.4
1641	40	26.6	26.6	26.6
2554	41	27.6	27.6	27.6
2554	42	23	23	23
1594	43	29.4	29.4	29.4
1594	44	25.8	25.8	25.8
1205	45	59.4	59.4	59.4
1205	46	45.4	45.4	45.4
2731	47	22.6	22.6	22.6
2731	48	17.2	17.2	17.2
1451	49	29	29	29
1451	50	45.8	45.6	45.7
1418	51	57.8	57.8	57.8
1418	52	45.4	45.4	45.4

Gel Electrophoresis Results:

TapeStation Results:

Coral ID	Extraction ID	RIN
2363	33	7.4
2363	34	7.5
1486	35	7.3
1486	36	7
1159	37	6.9
1159	38	6.5
1641	39	7.4
1641	40	6.8
2554	41	9.1
2554	42	8.6
1594	43	7.6
1594	44	7.8
1205	45	7.3
1205	46	7
2731	47	5.7
2731	48	**
1451	49	7.7
1451	50	7.7
1418	51	7.4
1418	52	7

** Concentration too low to read.
Not enough buffer in samples #35,36. Values in second report.

Link to 20190720 report #1, Extractions #33-52
Link to 20190720 report #2, Extractions #33-52
Link to Agilent 4200 TapeStation System