Soft and Hard Homogenization DNA/RNA Extractions #227-254

20190801 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.

Round 1: Extractions #227-242:
Fragment preparation start 10:00 end 10:15
Soft/Hard homogenization start 10:16 end NA
RNA DNA Extraction start NA end ~13:30

No time data for Round 2: Extractions #243-254

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

Elution 2 of the DNA extractions not measured on Qubit.

Round 1: Extractions #227-242:
DNA Standard 1: 196.29 ng/μl
DNA Standard 2: 21,117.67 ng/μl
RNA Standard 1: 399.45 ng/μl
RNA Standard 2: 9,024.70 ng/μl

Round 2: Extractions #243-254:
DNA Standard 1: 191.06 ng/μl
DNA Standard 2: 20,916.33 ng/μl
RNA Standard 1: 392.22 ng/μl
RNA Standard 2: 10,100.11 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
20180929	Montipora	1705	227	soft	16.3	16.1	16.2	60.2	59.8	60	8.7
20180929	Montipora	1705	228	hard	11.9	11.8	11.85	27.2	27.2	27.2	8.5
20181020	Montipora	1083	229	soft	8.42	8.38	8.4	22	21.8	21.9	9.4
20181020	Montipora	1083	230	hard	6.98	6.94	6.96	13.2	13.2	13.2	8.6
20180922	Montipora	2866	231	soft	14.8	14.7	14.75	46.4	46.4	46.4	8.8
20180922	Montipora	2866	232	hard	10.8	10.8	10.8	20.4	20.4	20.4	7.5
20180929	Pocillopora	1330	233	soft	25	24.8	24.9	110	110	110	8.3
20180929	Pocillopora	1330	234	hard	16.9	16.7	16.8	82.6	82.4	82.5	8.8
20180922	Pocillopora	1617	235	soft	24	24	24	91.8	91.6	91.7	8.5
20180922	Pocillopora	1617	236	hard	30	29.8	29.9	114	114	114	7.8
20180929	Montipora	1164	237	soft	15.2	15.1	15.15	46.4	45.8	46.1	7.9
20180929	Montipora	1164	238	hard	8.86	8.76	8.81	19.2	19	19.1	9.3
20180929	Pocillopora	2870	239	soft	39.2	39	39.1	129	129	129	8.9
20180929	Pocillopora	2870	240	hard	36.2	35.8	36	120	120	120	8.6
20180922	Pocillopora	1227	241	soft	15.5	15.3	15.4	99.8	98.8	99.3	6.9
20180922	Pocillopora	1227	242	hard	10.6	10.5	10.55	146	144	145	7.9
20180922	Montipora	2518	243	soft	14	13.8	13.9	18.4	18.2	18.3	9.2
20180922	Montipora	2518	244	hard	8.32	9.28	8.8	18	17.8	17.9	8.8
20180922	Montipora	1289	245	soft	7.44	7.4	7.42	14.6	14.2	14.4	**
20180922	Montipora	1289	246	hard	7.52	7.5	7.51	10.6	10.8	10.7	**
20180929	Pocillopora	2999	247	soft	54.2	54.2	54.2	106	105	105.5	7
20180929	Pocillopora	2999	248	hard	44	44	44	96	95.4	95.7	7
20180929	Montipora	1496	249	soft	12.2	12.1	12.15	18.4	18.2	18.3	8.8
20180929	Montipora	1496	250	hard	9.9	9.88	9.89	11.4	11.2	11.3	**
20181020	Pocillopora	1755	251	soft	19.3	19.2	19.25	57	56.4	56.7	8.2
20181020	Pocillopora	1755	252	hard	12.4	11.6	12	19.6	19.6	19.6	8.6
20181020	Montipora	1246	253	soft	19.1	18.9	19	28.4	28	28.2	8.8
20181020	Montipora	1246	254	hard	19.8	19.9	19.85	53.4	52.8	53.1	8.2

Link to 20190801 TapeStation report, Extractions #227-242

Extractions #243-254 ran on 20190802 with extractions #255-266.

Link to 20190802 TapeStation report, Extractions #255-266

Gel Electrophoresis Results: