Holobiont Integration November DNA RNA Extractions
November DNA RNA Extractions
20191105 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.
DNA Standard 1: 157.24 ng/μl
DNA Standard 2: 22,736.54 ng/μl
RNA Standard 1: 380.45 ng/μl
RNA Standard 2: 10,889.84 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 | 2731 | 519 | soft | 21.4 | 21.2 | 21.3 | 23.4 | 23.4 | 23.4 | 8.4 |
| 20180922 | Montipora | 2731 | 520 | hard | 25 | 24.8 | 24.9 | 15.8 | 15.8 | 15.8 | NA |
| 20181117 | Montipora | 1689 | 521 | soft | 10.3 | 10.3 | 10.3 | ** | ** | ** | 8.6 |
| 20181117 | Montipora | 1689 | 522 | hard | 6.34 | 6.3 | 6.32 | ** | ** | ** | NA |
| 20180922 | Montipora | 2021 | 523 | soft | 9.88 | 9.74 | 9.81 | 14.8 | 14.8 | 14.8 | 8.6 |
| 20180922 | Montipora | 2021 | 524 | hard | 9.68 | 9.66 | 9.67 | 10.8 | 11 | 10.9 | NA |
| 20181117 | Montipora | 1332 | 525 | soft | 9 | 8.98 | 8.99 | 14.8 | 14.8 | 14.8 | ** |
| 20181117 | Montipora | 1332 | 526 | hard | 9.82 | 9.76 | 9.79 | ** | ** | ** | NA |
| 20190112 | Montipora | 2736 | 527 | soft | 20.6 | 20.4 | 20.5 | 20 | 20 | 20 | 8.3 |
| 20190112 | Montipora | 2736 | 528 | hard | 11.3 | 11.2 | 11.25 | 13.8 | 14 | 13.9 | NA |
| 20190112 | Montipora | 1729 | 529 | soft | 28.8 | 28.8 | 28.8 | 23 | 23.2 | 23.1 | 9.1 |
| 20190112 | Montipora | 1729 | 530 | hard | 20 | 19.9 | 19.95 | 14.8 | 14.8 | 14.8 | NA |
| 20190112 | Montipora | 2403 | 531 | soft | 10.1 | 10 | 10.05 | 12.8 | 13 | 12.9 | 9.2 |
| 20190112 | Montipora | 2403 | 532 | hard | 7.3 | 7.28 | 7.29 | 10.2 | 10.2 | 10.2 | NA |
| 20190112 | Montipora | 2007 | 533 | soft | 18 | 17.9 | 17.95 | 11.4 | 11.6 | 11.5 | 9 |
| 20190112 | Montipora | 2007 | 534 | hard | 12.2 | 12.2 | 12.2 | 15.4 | 15.6 | 15.5 | NA |
| 20190112 | Montipora | 1154 | 535 | soft | 33.6 | 33.4 | 33.5 | 16.8 | 16.8 | 16.8 | 8.8 |
| 20190112 | Montipora | 1154 | 536 | hard | 13.2 | 13.1 | 13.15 | 12.6 | 12.6 | 12.6 | NA |
| 20190112 | Montipora | 1274 | 537 | soft | 28.2 | 28 | 28.1 | 22.6 | 22.6 | 22.6 | 8.9 |
| 20190112 | Montipora | 1274 | 538 | hard | 19.9 | 19.8 | 19.85 | 13.2 | 13.4 | 13.3 | NA |
Link to 20191109 TapeStation report, Extractions #519-538
20191111 E.S., A.M.
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).
Only one elution for DNA. All final DNA is in tubes labeled “DNA 1”.
Qubit used to check DNA and RNA quantity (ng/μl).
TapeStation used to check RNA quality.
High-Sensitivity:
DNA Standard 1: 147.66 ng/μl
DNA Standard 2: 19,556.29 ng/μl
RNA Standard 1: 52.66 ng/μl
RNA Standard 2: 970.15 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 20181103 | Pocillopora | 1302 | 539 | soft | 47.6 | 47 | 47.3 | 41.4 | 41.2 | 41.3 | 8.2 |
| 20181103 | Pocillopora | 1302 | 540 | hard | 15.6 | 15.5 | 15.55 | 19.8 | 19.8 | 19.8 | NA |
| 20180929 | Montipora | 1212 | 541 | soft | 10.6 | 10.6 | 10.6 | 8.96 | 8.98 | 8.97 | ** |
| 20180929 | Montipora | 1212 | 542 | hard | 6.96 | 6.92 | 6.94 | 5.46 | 5.46 | 5.46 | NA |
| 20180922 | Montipora | 1481 | 543 | soft | 20.2 | 20 | 20.1 | 11.7 | 11.6 | 11.65 | 8.3 |
| 20180922 | Montipora | 1481 | 544 | hard | 12.6 | 12.5 | 12.55 | 7.66 | 7.58 | 7.62 | NA |
| 20181020 | Montipora | 2067 | 545 | soft | 14.3 | 14.2 | 14.25 | 6.92 | 6.86 | 6.89 | ** |
| 20181020 | Montipora | 2067 | 546 | hard | 9.98 | 9.92 | 9.95 | 4.2 | 4.4 | 4.3 | NA |
| 20181020 | Montipora | 2410 | 547 | soft | 7.32 | 7.28 | 7.3 | 6.12 | 6.16 | 6.14 | 7.8 |
| 20181020 | Montipora | 2410 | 548 | hard | 7.4 | 7.36 | 7.38 | 5.14 | 5.14 | 5.14 | NA |
| 20180929 | Montipora | 2555 | 549 | soft | 24.8 | 24.8 | 24.8 | 21 | 21 | 21 | 9.1 |
| 20180929 | Montipora | 2555 | 550 | hard | 19.9 | 19.8 | 19.85 | 13.5 | 13.5 | 13.5 | NA |
| 20181117 | Montipora | 1315 | 551 | soft | 16.1 | 16.1 | 16.1 | 11.1 | 11 | 11.05 | 8.2 |
| 20181117 | Montipora | 1315 | 552 | hard | 9.66 | 9.62 | 9.64 | 6.6 | 6.7 | 6.65 | NA |
| 20181020 | Montipora | 2735 | 553 | soft | 27.8 | 27.8 | 27.8 | 18.3 | 18.3 | 18.3 | 9.1 |
| 20181020 | Montipora | 2735 | 554 | hard | 16.3 | 16.3 | 16.3 | 10.1 | 10 | 10.05 | NA |
| 20181103 | Montipora | 1121 | 555 | soft | 21.2 | 21 | 21.1 | 7.66 | 7.78 | 7.72 | 8.4 |
| 20181103 | Montipora | 1121 | 556 | hard | 13.3 | 13.2 | 13.25 | 12.4 | 12.5 | 12.45 | NA |
| 20181103 | Montipora | 2009 | 557 | soft | 85.8 | 85.6 | 85.7 | 13.6 | 13.6 | 13.6 | 9 |
| 20181103 | Montipora | 2009 | 558 | hard | 30.6 | 30.6 | 30.6 | 38.6 | 38.4 | 38.5 | NA |
Link to 20191113 TapeStation report, Extractions #539-558
20191113 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: 41.06 ng/μl
DNA Standard 2: 20,514.38 ng/μl
RNA Standard 1: 51.27 ng/μl
RNA Standard 2: 1,003.4 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 | Pocillopora | 2534 | 559 | soft | 69.6 | 69.2 | 69.4 | 39.4 | 39.6 | 39.5 | 6.9 |
| 20180922 | Pocillopora | 2534 | 560 | hard | 38.6 | 38.6 | 38.6 | 19.6 | 19.6 | 19.6 | NA |
| 20180922 | Montipora | 1609 | 561 | soft | ** | ** | ** | 34 | 34 | 34 | 8.2 |
| 20180922 | Montipora | 1609 | 562 | hard | 42.4 | 42.4 | 42.4 | ** | ** | ** | NA |
| 20180922 | Montipora | 1628 | 563 | soft | 48 | 47.8 | 47.9 | 44.8 | 45.2 | 45 | 8.1 |
| 20180922 | Montipora | 1628 | 564 | hard | 26.2 | 26.2 | 26.2 | 22.2 | 22.2 | 22.2 | NA |
| 20180922 | Pocillopora | 2733 | 565 | soft | 48.6 | 48.6 | 48.6 | 23.6 | 23.6 | 23.6 | 6.7 |
| 20180922 | Pocillopora | 2733 | 566 | hard | 32.8 | 32.8 | 32.8 | 14.1 | 14.2 | 14.15 | NA |
| 20180922 | Montipora | 1169 | 567 | soft | 40.8 | 40.8 | 40.8 | 46.2 | 46.2 | 46.2 | 7.9 |
| 20180922 | Montipora | 1169 | 568 | hard | 28.4 | 28.4 | 28.4 | 26.4 | 26.4 | 26.4 | NA |
| 20180922 | Montipora | 1289 | 569 | soft | 24 | 23.8 | 23.9 | 14.1 | 14.1 | 14.1 | 8.6 |
| 20180922 | Montipora | 1289 | 570 | hard | 14.3 | 14.3 | 14.3 | 7.92 | 7.9 | 7.91 | NA |
| 20181117 | Montipora | 1204 | 571 | soft | 14.3 | 14.3 | 14.3 | 5.46 | 5.42 | 5.44 | ** |
| 20181117 | Montipora | 1204 | 572 | hard | 9.68 | 9.66 | 9.67 | 5.4 | 5.42 | 5.41 | NA |
| 20180922 | Montipora | 1124 | 573 | soft | 27.8 | 27.8 | 27.8 | 16.7 | 16.6 | 16.65 | 8.8 |
| 20180922 | Montipora | 1124 | 574 | hard | 18.9 | 18.9 | 18.9 | 10.2 | 10.2 | 10.2 | NA |
Link to 20191115 TapeStation report, Extractions #539-558
20191121 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: 46.36 ng/μl
DNA Standard 2: 20,805.39 ng/μl
RNA Standard 1: 51.69 ng/μl
RNA Standard 2: 1,024.6 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 | 1221 | 575 | soft | 18.9 | 18.7 | 18.8 | 18.9 | 19 | 18.95 | 8.4 |
| 20180922 | Montipora | 1221 | 576 | hard | 11.7 | 11.6 | 11.65 | 8.34 | 8.34 | 8.34 | NA |
| 20180922 | Montipora | 1108 | 577 | soft | 21 | 20.8 | 20.9 | 10.9 | 10.9 | 10.9 | 8.7 |
| 20180922 | Montipora | 1108 | 578 | hard | 13.2 | 13.1 | 13.15 | 6.28 | 6.24 | 6.26 | NA |
| 20180922 | Pocillopora | 2195 | 579 | soft | 71.4 | 71.2 | 71.3 | 38.4 | 38.2 | 38.3 | 8.3 |
| 20180922 | Pocillopora | 2195 | 580 | hard | 30 | 30 | 30 | 16.4 | 16.4 | 16.4 | NA |
| 20180923 | Pocillopora | 1571 | 581 | soft | 61.6 | 61.4 | 61.5 | 29.2 | 29.2 | 29.2 | 8.2 |
| 20180923 | Pocillopora | 1571 | 582 | hard | 25.8 | 25.6 | 25.7 | 18.4 | 18.4 | 18.4 | NA |
| 20180922 | Pocillopora | 1762 | 583 | soft | 20.4 | 20.4 | 20.4 | 16.7 | 16.8 | 16.75 | 9.1 |
| 20180922 | Pocillopora | 1762 | 584 | hard | 18.9 | 18.8 | 18.85 | 14.6 | 14.6 | 14.6 | NA |
| 20181103 | Montipora | 1467 | 585 | soft | 22 | 22 | 22 | 8.4 | 8.34 | 8.37 | 8.6 |
| 20181103 | Montipora | 1467 | 586 | hard | 10.5 | 10.5 | 10.5 | 4.6 | 4.8 | 4.7 | NA |
| 20180929 | Pocillopora | 1468 | 587 | soft | 26.8 | 26.8 | 26.8 | 35.8 | 35.8 | 35.8 | 8.4 |
| 20180929 | Pocillopora | 1468 | 588 | hard | 10 | 10 | 10 | 18.7 | 18.7 | 18.7 | NA |
| 20180923 | Montipora | 1321 | 589 | soft | 13.9 | 13.8 | 13.85 | 14 | 13.9 | 13.95 | 9.3 |
| 20180923 | Montipora | 1321 | 590 | hard | 8.94 | 8.9 | 8.92 | ** | ** | ** | NA |
| 20181020 | Pocillopora | 1709 | 591 | soft | 28.8 | 28.8 | 28.8 | 44 | 44 | 44 | 8.9 |
| 20181020 | Pocillopora | 1709 | 592 | hard | 20 | 20 | 20 | 21.6 | 21.4 | 21.5 | NA |
| 20180923 | Montipora | 1583 | 593 | soft | 21.2 | 21.2 | 21.2 | 11 | 11.1 | 11.05 | 8.9 |
| 20180923 | Montipora | 1583 | 594 | hard | 12 | 12 | 12 | 6.38 | 6.42 | 6.4 | NA |
Link to 20191126 TapeStation report, Extractions #575-594
20191125 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: 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 | 2737 | 595 | soft | 22.2 | 22 | 22.1 | 19.5 | 19.5 | 19.5 | 8.9 |
| 20181117 | Montipora | 2737 | 596 | hard | 12.1 | 12 | 12.05 | 11.6 | 11.6 | 11.6 | NA |
| 20181103 | Montipora | 1078 | 597 | soft | 15.7 | 15.6 | 15.65 | 9.84 | 9.76 | 9.8 | 8.4 |
| 20181103 | Montipora | 1078 | 598 | hard | 9.48 | 9.44 | 9.46 | 5.36 | 5.42 | 5.39 | NA |
| 20180923 | Montipora | 1610 | 599 | soft | 12.6 | 12.6 | 12.6 | 11.3 | 11.5 | 11.4 | 8.8 |
| 20180923 | Montipora | 1610 | 600 | hard | 9.32 | 9.3 | 9.31 | 6.86 | 6.8 | 6.83 | NA |
| 20180929 | Montipora | 1604 | 601 | soft | 11.6 | 11.6 | 11.6 | 10.6 | 10.6 | 10.6 | 8.5 |
| 20180929 | Montipora | 1604 | 602 | hard | 6.64 | 6.62 | 6.63 | 5.94 | 5.86 | 5.9 | NA |
| 20180929 | Montipora | 2016 | 603 | soft | 22.2 | 22.2 | 22.2 | 26.4 | 26.4 | 26.4 | 8.6 |
| 20180929 | Montipora | 2016 | 604 | hard | 16 | 15.9 | 15.95 | 9.4 | 9.38 | 9.39 | NA |
Link to 20191204 TapeStation report, Extractions #595-604
