December DNA RNA Extractions

20191202 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).

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

High Sensitivity:
DNA Standard 1: 56.40 ng/μl
DNA Standard 2: 24,393.58 ng/μl
RNA Standard 1: 50.42 ng/μl
RNA Standard 2: 1,012.40 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
20180922	Montipora	1269	605	soft	23	23	23	16.8	16.7	16.75	8.6
20180922	Montipora	1269	606	hard	9.28	9.26	9.27	8.9	9	8.95	NA
20181006	Montipora	1722	607	soft	26.4	26.4	26.4	37.2	37	37.1	8.9
20181006	Montipora	1722	608	hard	18.4	18.4	18.4	11.2	11.3	11.25	NA
20181006	Montipora	1455	609	soft	19.6	19.5	19.55	17.4	17.5	17.45	9.1
20181006	Montipora	1455	610	hard	12.5	12.4	12.45	10.2	10.2	10.2	NA
20181215	Montipora	2511	611	soft	10.7	10.6	10.65	9.56	9.58	9.57	8.7
20181215	Montipora	2511	612	hard	5.12	5.1	5.11	6.58	6.46	6.52	NA
20181006	Montipora	1645	613	soft	10.7	10.6	10.65	11.4	11.4	11.4	8.7
20181006	Montipora	1645	614	hard	3.44	3.44	3.44	9.28	9.32	9.3	NA
20180929	Montipora	1588	615	soft	11.3	11.2	11.25	12.3	12.4	12.35	9
20180929	Montipora	1588	616	hard	7.62	7.58	7.6	8.54	8.52	8.53	NA
20180923	Montipora	1229	617	soft	8.92	8.9	8.91	12	12	12	8.7
20180923	Montipora	1229	618	hard	14	14	14	10.7	10.7	10.7	NA
20180922	Montipora	1277	619	soft	19.6	19.5	19.55	15.9	16	15.95	8.9
20180922	Montipora	1277	620	hard	14.7	14.7	14.7	15.2	15.2	15.2	NA
20180922	Montipora	1236	621	soft	0.3	0.288	0.294	9.28	9.28	9.28	**
20180922	Montipora	1236	622	hard	0.228	0.22	0.224	7.58	7.62	7.6	NA
20181215	Pocillopora	1147	623	soft	82	82	82	116	116	116	7
20181215	Pocillopora	1147	624	hard	42.2	42.2	42.2	48.6	48.4	48.5	NA

Link to 20191204 TapeStation report, Extractions #605-624

Gel Electrophoresis Results:

20191204 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).

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

High Sensitivity:
DNA Standard 1: 56.40 ng/μl
DNA Standard 2: 24,393.58 ng/μl
RNA Standard 1: 50.42 ng/μl
RNA Standard 2: 1,012.40 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
20181117	Montipora	1315	625	soft	43.8	43.6	43.7	23.8	23.6	23.7	8.5
20181117	Montipora	1315	626	hard	23.8	23.8	23.8	14.9	14.8	14.85	NA
20190112	Montipora	2403	627	soft	24.8	24.8	24.8	7.64	7.7	7.67	**
20190112	Montipora	2403	628	hard	15.9	15.9	15.9	6.62	6.72	6.67	NA
20181020	Montipora	1083	629	soft	21.8	21.8	21.8	15.3	15.4	15.35	8.6
20181020	Montipora	1083	630	hard	25.4	25.4	25.4	9.08	9.12	9.1	NA
20181020	Montipora	2067	631	soft	16.1	16.1	16.1	8.4	8.46	8.43	8.4
20181020	Montipora	2067	632	hard	18.6	18.4	18.5	6.56	6.52	6.54	NA
20181215	Montipora	2380	633	soft	23.2	23	23.1	18.9	18.8	18.85	8.8
20181215	Montipora	2380	634	hard	22.4	22.4	22.4	14.6	14.6	14.6	NA
20181020	Montipora	2410	635	soft	35.8	35.6	35.7	12.1	12.1	12.1	8.5
20181020	Montipora	2410	636	hard	18.2	18.2	18.2	8.68	8.6	8.64	NA
20180922	Montipora	2021	637	soft	51.2	51.2	51.2	17.7	17.6	17.65	8.5
20180922	Montipora	2021	638	hard	11.1	11	11.05	16.4	16.3	16.35	NA
20180922	Montipora	1121	639	soft	30.2	30	30.1	16.9	16.9	16.9	8.7
20180922	Montipora	1121	640	hard	20.4	20.4	20.4	10.8	10.8	10.8	NA
20181020	Pocillopora	1329	641	soft	41.8	41.6	41.7	48	48	48	8.7
20181020	Pocillopora	1329	642	hard	48.2	48	48.1	36.4	36.6	36.5	NA
20181117	Montipora	1689	643	soft	10.6	10.6	10.6	6.7	6.7	6.7	7.9	s
20181117	Montipora	1689	644	hard	9.04	9	9.02	5.4	5.36	5.38	NA

Link to 20191205 TapeStation report, Extractions #625-644

Gel Electrophoresis Results:

20191205 M.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).

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

High Sensitivity:
DNA Standard 1: 47.64 ng/μl
DNA Standard 2: 25,437.24 ng/μl
RNA Standard 1: 52.52 ng/μl
RNA Standard 2: 1,057.21 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
20181117	Montipora	1332	645	soft	43.4	43.2	43.3	19.9	19.9	19.9	7.9
20181117	Montipora	1332	646	hard	22.2	22.2	22.2	9.4	9.44	9.42	NA
20180929	Montipora	1212	647	soft	34	34	34	22.4	22.4	22.4	8.4
20180929	Montipora	1212	648	hard	24.2	24.2	24.2	14.2	14.1	14.15	NA
20181020	Montipora	3753	649	soft	46	46	46	28.6	28.6	28.6	8.9
20181020	Montipora	3753	650	hard	17.9	17.9	17.9	11	11	11	NA
20180922	Montipora	1481	651	soft	40.6	40.4	40.5	24	24	24	8.2
20180922	Montipora	1481	652	hard	19.7	19.6	19.65	11.8	11.8	11.8	NA

Link to 20191205 TapeStation report, Extractions #645-652

Gel Electrophoresis Results:

20191206 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).

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

Broad Range:
DNA Standard 1: 154.57 ng/μl
DNA Standard 2: 22,496.94 ng/μl

High Sensitivity:
RNA Standard 1: 51.33 ng/μl
RNA Standard 2: 977.46 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	1645	653	soft	17.2	17.2	17.2	8.14	8.2	8.17	7.8
20181006	Montipora	1645	654	hard	14.5	14.4	14.45	7.02	7	7.01	NA
20180929	Montipora	1588	655	soft	10.7	10.6	10.65	12.8	12.7	12.75	8.3
20180929	Montipora	1588	656	hard	14.3	14.3	14.3	8.6	8.58	8.59	NA
20181215	Montipora	2511	657	soft	19.8	19.7	19.75	16.7	16.6	16.65	7.9
20181215	Montipora	2511	658	hard	16.1	16.1	16.1	14.1	14.1	14.1	NA
20181215	Pocillopora	1147	659	soft	57.6	57.4	57.5	120	120	120	6.7
20181215	Pocillopora	1147	660	hard	39.4	39.2	39.3	69	69	69	NA
20180923	Montipora	1229	661	soft	14.8	14.7	14.75	12.6	12.6	12.6	8.4
20180923	Montipora	1229	662	hard	11.9	11.8	11.85	11.1	11	11.05	NA
20181117	Montipora	1689	663	soft	35	34.8	34.9	16.1	16.1	16.1	7.6
20181117	Montipora	1689	664	hard	20.4	20.4	20.4	13.4	13.5	13.45	NA

Link to 20191206 TapeStation report, Extractions #653-664

Gel Electrophoresis Results:

check notebook post for gel map.

20191208 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).

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

High Sensitivity:
DNA Standard 1: X ng/μl
DNA Standard 2: X ng/μl
RNA Standard 1: X ng/μl
RNA Standard 2: X 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
20181117	Montipora	1204	665	soft	35	34.8	34.9	30.6	30.8	30.7	8.3
20181117	Montipora	1204	666	hard	18.9	18.8	18.85	10.7	10.7	10.7	NA
20180922	Montipora	1609	667	soft	26	25.8	25.9	18.9	18.9	18.9	8.4
20180922	Montipora	1609	668	hard	12.5	12.4	12.45	10.2	10.2	10.2	NA
20180922	Pocillopora	2534	669	soft	105	104	104.5	108	108	108	7.4
20180922	Pocillopora	2534	670	hard	48.8	48.6	48.7	50.6	50.6	50.6	NA
20190112	Montipora	2403	671	soft	34.6	34.4	34.5	31.8	31.8	31.8	8.9
20190112	Montipora	2403	672	hard	20.8	20.8	20.8	13.2	13.2	13.2	NA
20181020	Montipora	2067	673	soft	16.5	16.4	16.45	5.02	5.08	5.05	**
20181020	Montipora	2067	674	hard	9.74	9.68	9.71	4	4	4	NA

Link to 20191209 TapeStation report, Extractions #665-674

Gel Electrophoresis Results:

20191209 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).

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

Broad Range:
DNA Standard 1: 157.25 ng/μl
DNA Standard 2: 22,162.92 ng/μl

High Sensitivity:
RNA Standard 1: 50.97 ng/μl
RNA Standard 2: 1,111.48 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
20181215	Pocillopora	1147	675	soft	54	53.8	53.9	54.8	54.8	54.8	5.9
20181215	Pocillopora	1147	676	hard	19.5	19.5	19.5	19.8	19.8	19.8	NA
20180923	Montipora	1321	677	soft	37.4	37.2	37.3	35.2	35.2	35.2	9
20180923	Montipora	1321	678	hard	16.9	16.8	16.85	13.5	13.5	13.5	NA
20180929	Montipora	1604	679	soft	29.2	29	29.1	18.8	18.8	18.8	8.1
20180929	Montipora	1604	680	hard	30.6	30.4	30.5	13.4	13.4	13.4	NA
20181006	Montipora	1645	681	soft	30.4	30.2	30.3	23.8	23.8	23.8	8.9
20181006	Montipora	1645	682	hard	20.6	20.4	20.5	14.3	14.3	14.3	NA
20181020	Montipora	2067	683	soft	24.8	24.6	24.7	10.8	10.8	10.8	8.6
20181020	Montipora	2067	684	hard	13	13	13	5.9	5.84	5.87	NA

Link to 20191209 TapeStation report, Extractions #675-679

Link to 20191209 TapeStation report, Extractions #681-684

Gel Electrophoresis Results:

20191210 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).

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

Broad Range: DNA Standard 1: 130.12 ng/μl
DNA Standard 2: 17,735.30 ng/μl

High Sensitivity: RNA Standard 1: 51.16 ng/μl
RNA Standard 2: 1,024.51 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
20190112	Montipora	2990	685	soft	28.4	28	28.2	16.6	16.6	16.6	8.3
20190112	Montipora	2990	686	hard	15.2	15	15.1	12.7	12.6	12.65	NA
20180923	Montipora	2986	687	soft	12	11.9	11.95	15.6	15.5	15.55	8.7
20180923	Montipora	2986	688	hard	10.4	10.3	10.35	8.32	8.24	8.28	NA
20180922	Montipora	2153	689	soft	37.2	36.6	36.9	38.2	38	38.1	9
20180922	Montipora	2153	690	hard	21.2	20.8	21	15.7	15.7	15.7	NA
20181103	Montipora	1467	691	soft	28.4	27.8	28.1	15.6	15.5	15.55	8.6
20181103	Montipora	1467	692	hard	12.9	12.6	12.75	8.62	8.54	8.58	NA

Link to 20191210 TapeStation report, Extractions #685-692

Gel Electrophoresis Results:

20191216 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).

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

Broad Range: DNA Standard 1: 164 ng/μl
DNA Standard 2: 23,368 ng/μl

High Sensitivity: RNA Standard 1: 50.53 ng/μl
RNA Standard 2: 1,061 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
20180922	Montipora	2734	693	soft	38.8	38.6	38.7	4.8	4.6	4.7
20180922	Montipora	2734	694	hard	21	21	21	**	**	**	NA

Re-extraction:

Broad Range: DNA Standard 1: 166 ng/μl
DNA Standard 2: 23,551 ng/μl

High Sensitivity: RNA Standard 1: 53.50 ng/μl
RNA Standard 2: 1,065 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
20180922	Montipora	2734	695	soft	74.2	73	73.6	54.6	54.2	54.4	8.3
20180922	Montipora	2734	696	hard	35.4	34	34.7	22.4	22.4	22.4	NA

Tubes labeled as extraction IDs 685, 686, 687, 688. The correct extraction IDs are 693, 694, 695, 696.

Link to 20191216 TapeStation report, Extractions #695

Gel Electrophoresis Results: