Soft and Hard Homogenization DNA/RNA Extractions #395-416

20190827 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.

Extraction numbers #399 and #400 not used. No corals or tubes assigned to #399 or #400.

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

DNA Standard 1: 183.02 ng/μl
DNA Standard 2: 22,986.92 ng/μl
RNA Standard 1: 410.43 ng/μl
RNA Standard 2: 10,577.53 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	1652	395	soft	23.4	23.4	23.4	29.6	29.6	29.6	9.1
20180922	Montipora	1652	396	hard	7.4	7.38	7.39	18.8	18.8	18.8	NA
20180922	Montipora	1218	397	soft	19.6	19.5	19.55	30.6	30.6	30.6	9.1
20180922	Montipora	1218	398	hard	13.4	13.4	13.4	15.2	15.4	15.3	NA
20180922	Montipora	1037	401	soft	18.9	18.9	18.9	14.4	14.4	14.4	8.3
20180922	Montipora	1037	402	hard	9.38	9.34	9.36	11	11	11	NA
20180922	Pocillopora	1701	403	soft	107	107	107	109	110	109.5	8.7
20180922	Pocillopora	1701	404	hard	34.2	34.2	34.2	77	77	77	NA
20180922	Pocillopora	1581	405	soft	43.2	43.2	43.2	70.8	70.8	70.8	8.8
20180922	Pocillopora	1581	406	hard	37.2	37.2	37.2	52.2	52.2	52.2	NA
20180922	Montipora	1328	407	soft	24.2	22.8	23.5	27.2	27	27.1	9.1
20180922	Montipora	1328	408	hard	13.7	13.7	13.7	19.8	19.8	19.8	NA
20180923	Montipora	1706	409	soft	12	12	12	14.4	14.4	14.4	8.8
20180923	Montipora	1706	410	hard	10.7	11	10.85	12.2	12.2	12.2	NA
20180923	Montipora	2986	411	soft	17.9	17.8	17.85	10	10	10	**
20180923	Montipora	2986	412	hard	10.3	10.2	10.25	11.6	11.8	11.7	NA
20180923	Pocillopora	1059	413	soft	27	27	27	73.2	73.2	73.2	9.2
20180923	Pocillopora	1059	414	hard	25.2	25.2	25.2	48	48	48	NA
20180923	Pocillopora	2087	415	soft	50.6	50.4	50.5	80.6	80.6	80.6	8.9
20180923	Pocillopora	2087	416	hard	35.4	35.2	35.3	70.8	70.8	70.8	NA

Link to 20190827 TapeStation report, Extractions #395-416

#315 and #313 on the TapeStation are mislabeled. Those samples are #413 and #415.

Gel Electrophoresis Results:

The last lane is a re-do of Extraction #402 because the first lane mostly floated out of the well.