Soft and Hard Homogenization DNA/RNA Extractions #303-322

20190807 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. With the following changes:

• DNA: The first and second elutions were spun down in separate microcentrifuge tubes to compare the quantity and quality between the first and second elution. The first elution had no incubation period (previously 5 minutes) with 10 μl of Tris buffer and the second elution had a 15 minute incubation period (previously 5 minutes) with 100 μl of Tris buffer.
• 10 μl aliquots of DNA and 5 μl aliquots of RNA (instead of 10 μl of each).

Coral fragments were randomly chosen from different timepoint bags.

Fragment preparation start 11:28 end 12:07
Soft/Hard homogenization start 12:08 end NA
RNA DNA Extraction start NA end 15:15

Qubit used to check DNA and RNA quantity (ng/μl).
TapeStation used to check RNA quality.

DNA Standard 1: 193.68 ng/μl
DNA Standard 2: 19,619.20 ng/μl
RNA Standard 1: 390.76 ng/μl
RNA Standard 2: 10,145.65 ng/μl

Timepoint	Species	Coral ID	Extraction ID	Homogenization	DNA Reading 1	DNA Reading 2	Average DNA ng/μl	RNA Reading 1	RNA Reading 2	Average RNA ng/μl	RIN
20181006	Montipora	2860	303	soft	43.8	43.2	43.5	45.2	45	45.1	9.1
20181006	Montipora	2860	304	hard	17.8	17.7	17.75	23.8	23.6	23.7	9
20181006	Montipora	1126	305	soft	19.1	19.1	19.1	30.8	30.6	30.7	8.7
20181006	Montipora	1126	306	hard	13.4	13.4	13.4	16.6	16.6	16.6	8.8
20180922	Montipora	2204	307	soft	21.4	21.4	21.4	41.4	41.4	41.4	8.6
20180922	Montipora	2204	308	hard	11.5	11.4	11.45	33.6	33.2	33.4	9.1
20180929	Pocillopora	1744	309	soft	27.4	27.4	27.4	83.8	83.4	83.6	8.4
20180929	Pocillopora	1744	310	hard	21.8	21.8	21.8	40.4	40.2	40.3	8.2
20181006	Pocillopora	1427	311	soft	43	42.8	42.9	52.4	52.2	52.3	8.8
20181006	Pocillopora	1427	312	hard	29.8	29.6	29.7	34.4	34.2	34.3	8.5
20181006	Pocillopora	1090	313	soft	31.6	31.4	31.5	30.6	30.6	30.6	8.4
20181006	Pocillopora	1090	314	hard	14	14	14	25.4	25.4	25.4	8.1
20180922	Montipora	1323	315	soft	19.5	19.5	19.5	23.4	23.4	23.4	9.2
20180922	Montipora	1323	316	hard	10.8	10.7	10.75	17	17	17	**
20181006	Pocillopora	1487	317	soft	37.4	37.2	37.3	69	68.6	68.8	7.4
20181006	Pocillopora	1487	318	hard	36.2	36	36.1	34	33.8	33.9	7.3
20181006	Pocillopora	2878	319	soft	48.2	48	48.1	59	58.8	58.9	8.2
20181006	Pocillopora	2878	320	hard	48.8	48.6	48.7	50.4	50.2	50.3	7.9
20180922	Pocillopora	2414	321	soft	63.8	63.6	63.7	112	112	112	8.6
20180922	Pocillopora	2414	322	hard	48	48	48	59.4	59.2	59.3	8.2

Not enough TapeStation tips to run today’s samples.

Gel Electrophoresis Results:

20190809 edit:

Link to 20190809 TapeStation report, Extractions #290-342

Coral ID	Extraction ID	RIN
1269	290	9
1826	291	8.9
1826	292	9
1728	293	8.1
1728	294	8.2
1544	295	8.8
1544	296	8.9
1223	297	9.2
1223	298	**
1611	299	8.8
1611	300	8.9
2875	301	NA
2875	302	8.7
2860	303	9.1
2860	304	9
1126	305	8.7
1126	306	8.8
2204	307	8.6
2204	308	9.1
1744	309	8.4
1744	310	8.2
1427	311	8.8
1427	312	8.5
1090	313	NA
1090	314	8.1
1323	315	9.2
1323	316	**
1487	317	7.4
1487	318	7.3
2878	319	8.2
2878	320	7.9
2414	321	8.6
2414	322	8.2
2409	323	8.2
2409	324	7.8
1047	325	NA
1047	326	7.8
1595	327	8.5
1595	328	8.6
1499	329	9
1499	330	8.7
2068	331	8.7
2068	332	**

Extractions #: 301, 313, 325, and 337 did not run because not enough TapeStation screentapes.

20190812 edit:

TapeStation ran for Extraction ID #s: 301, 313, 325, and 337.

Link to 20190812 TapeStation report, Extractions #301, 313, 325, 337