Soft and Hard Homogenization Extractions
Soft and Hard Homogenization DNA/RNA Extractions #179-226
20190731 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 #179-202
Fragment preparation start 8:00 end 8:35
Soft/Hard homogenization start 8:36 end 9:17
RNA DNA Extraction start 9:18 end ~12:30
Qubit used to check DNA and RNA quantity (ng/μl).
TapeStation used to check RNA quality.
DNA Standard 1: 208.49 ng/μl
DNA Standard 2: 24255.12 ng/μl
RNA Standard 1: 393.41 ng/μl
RNA Standard 2: 7871.22 ng/μl
| Timepoint | Species | Coral ID | Extraction ID | Homogenization | DNA Elution | DNA Reading 1 | DNA Reading 2 | Average DNA ng/μl | RNA Reading 1 | RNA Reading 2 | Average RNA ng/μl | RIN |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 20181020 | Montipora | 2410 | 179 | soft | NA | NA | NA | NA | 16 | 15.8 | 15.9 | ** |
| 20181020 | Montipora | 2410 | 179-1 | soft | 1 | 83.4 | 82.6 | 83 | NA | NA | NA | NA |
| 20181020 | Montipora | 2410 | 179-2 | soft | 2 | 13.2 | 13 | 13.1 | NA | NA | NA | NA |
| 20181020 | Montipora | 2410 | 180 | hard | NA | NA | NA | NA | 12.2 | 12 | 12.1 | ** |
| 20181020 | Montipora | 2410 | 180-1 | hard | 1 | 13 | 12.9 | 12.95 | NA | NA | NA | NA |
| 20181020 | Montipora | 2410 | 180-2 | hard | 2 | 8.7 | 8.6 | 8.65 | NA | NA | NA | NA |
| 20181117 | Pocillopora | 2300 | 181 | soft | NA | NA | NA | NA | 71.2 | 71 | 71.1 | 8.3 |
| 20181117 | Pocillopora | 2300 | 181-1 | soft | 1 | 312 | 308 | 310 | NA | NA | NA | NA |
| 20181117 | Pocillopora | 2300 | 181-2 | soft | 2 | 62.2 | 62 | 62.1 | NA | NA | NA | NA |
| 20181117 | Pocillopora | 2300 | 182 | hard | NA | NA | NA | NA | 60.4 | 59.6 | 60 | 8.6 |
| 20181117 | Pocillopora | 2300 | 182-1 | hard | 1 | 120 | 119 | 119.5 | NA | NA | NA | NA |
| 20181117 | Pocillopora | 2300 | 182-2 | hard | 2 | 33.4 | 33.2 | 33.3 | NA | NA | NA | NA |
| 20181020 | Pocillopora | 1184 | 183 | soft | NA | NA | NA | NA | 85 | 84.8 | 84.9 | 8 |
| 20181020 | Pocillopora | 1184 | 183-1 | soft | 1 | 199 | 198 | 198.5 | NA | NA | NA | NA |
| 20181020 | Pocillopora | 1184 | 183-2 | soft | 2 | 49.2 | 48.8 | 49 | NA | NA | NA | NA |
| 20181020 | Pocillopora | 1184 | 184 | hard | NA | NA | NA | NA | 59.8 | 59.8 | 59.8 | 8.1 |
| 20181020 | Pocillopora | 1184 | 184-1 | hard | 1 | 50.2 | 49.8 | 50 | NA | NA | NA | NA |
| 20181020 | Pocillopora | 1184 | 184-2 | hard | 2 | 34.2 | 33.2 | 33.7 | NA | NA | NA | NA |
| 20181020 | Montipora | 2735 | 185 | soft | NA | NA | NA | NA | 18.6 | 18.8 | 18.7 | ** |
| 20181020 | Montipora | 2735 | 185-1 | soft | 1 | 20.8 | 20.6 | 20.7 | NA | NA | NA | NA |
| 20181020 | Montipora | 2735 | 185-2 | soft | 2 | 6.8 | 6.68 | 6.74 | NA | NA | NA | NA |
| 20181020 | Montipora | 2735 | 186 | hard | NA | NA | NA | NA | 16.4 | 16.2 | 16.3 | ** |
| 20181020 | Montipora | 2735 | 186-1 | hard | 1 | 18.3 | 18.2 | 18.25 | NA | NA | NA | NA |
| 20181020 | Montipora | 2735 | 186-2 | hard | 2 | 8.54 | 8.42 | 8.48 | NA | NA | NA | NA |
| 20180923 | Montipora | 1345 | 187 | soft | NA | NA | NA | NA | 56.2 | 56.2 | 56.2 | 8.4 |
| 20180923 | Montipora | 1345 | 187-1 | soft | 1 | 37.8 | 37.8 | 37.8 | NA | NA | NA | NA |
| 20180923 | Montipora | 1345 | 187-2 | soft | 2 | 25.6 | 25.4 | 25.5 | NA | NA | NA | NA |
| 20180923 | Montipora | 1345 | 188 | hard | NA | NA | NA | NA | 41.8 | 41.8 | 41.8 | 9 |
| 20180923 | Montipora | 1345 | 188-1 | hard | 1 | 169 | 169 | 169 | NA | NA | NA | NA |
| 20180923 | Montipora | 1345 | 188-2 | hard | 2 | 23.6 | 23.4 | 23.5 | NA | NA | NA | NA |
| 20181103 | Montipora | 1078 | 189 | soft | NA | NA | NA | NA | 12.2 | 12 | 12.1 | ** |
| 20181103 | Montipora | 1078 | 189-1 | soft | 1 | 9.32 | 9.2 | 9.26 | NA | NA | NA | NA |
| 20181103 | Montipora | 1078 | 189-2 | soft | 2 | 2.66 | 2.56 | 2.61 | NA | NA | NA | NA |
| 20181103 | Montipora | 1078 | 190 | hard | NA | NA | NA | NA | ** | ** | ** | ** |
| 20181103 | Montipora | 1078 | 190-1 | hard | 1 | 2.76 | 2.82 | 2.79 | NA | NA | NA | NA |
| 20181103 | Montipora | 1078 | 190-2 | hard | 2 | ** | ** | ** | NA | NA | NA | NA |
| 20181117 | Montipora | 1315 | 191 | soft | NA | NA | NA | NA | ** | ** | ** | ** |
| 20181117 | Montipora | 1315 | 191-1 | soft | 1 | 5.44 | 5.38 | 5.41 | NA | NA | NA | NA |
| 20181117 | Montipora | 1315 | 191-2 | soft | 2 | ** | ** | ** | NA | NA | NA | NA |
| 20181117 | Montipora | 1315 | 192 | hard | NA | NA | NA | NA | ** | ** | ** | ** |
| 20181117 | Montipora | 1315 | 192-1 | hard | 1 | ** | ** | ** | NA | NA | NA | NA |
| 20181117 | Montipora | 1315 | 192-2 | hard | 2 | ** | ** | ** | NA | NA | NA | NA |
| 20181103 | Montipora | 2412 | 193 | soft | NA | NA | NA | NA | 45.6 | 45.4 | 45.5 | 8.6 |
| 20181103 | Montipora | 2412 | 193-1 | soft | 1 | 199 | 198 | 198.5 | NA | NA | NA | NA |
| 20181103 | Montipora | 2412 | 193-2 | soft | 2 | 21.6 | 20.8 | 21.2 | NA | NA | NA | NA |
| 20181103 | Montipora | 2412 | 194 | hard | NA | NA | NA | NA | 28.2 | 28.2 | 28.2 | 8.6 |
| 20181103 | Montipora | 2412 | 194-1 | hard | 1 | 68.6 | 68.4 | 68.5 | NA | NA | NA | NA |
| 20181103 | Montipora | 2412 | 194-2 | hard | 2 | 15.2 | 15.1 | 15.15 | NA | NA | NA | NA |
| 20180923 | Montipora | 1610 | 195 | soft | NA | NA | NA | NA | 17.8 | 17.6 | 17.7 | ** |
| 20180923 | Montipora | 1610 | 195-1 | soft | 1 | 11.1 | 11 | 11.05 | NA | NA | NA | NA |
| 20180923 | Montipora | 1610 | 195-2 | soft | 2 | 5.94 | 5.78 | 5.86 | NA | NA | NA | NA |
| 20180923 | Montipora | 1610 | 196 | hard | NA | NA | NA | NA | 19.6 | 19.4 | 19.5 | ** |
| 20180923 | Montipora | 1610 | 196-1 | hard | 1 | 14.5 | 14.4 | 14.45 | NA | NA | NA | NA |
| 20180923 | Montipora | 1610 | 196-2 | hard | 2 | 4.96 | 4.82 | 4.89 | NA | NA | NA | NA |
| 20180923 | Pocillopora | 1757 | 197 | soft | NA | NA | NA | NA | 97 | 96.6 | 96.8 | 8.6 |
| 20180923 | Pocillopora | 1757 | 197-1 | soft | 1 | 77.4 | 77.4 | 77.4 | NA | NA | NA | NA |
| 20180923 | Pocillopora | 1757 | 197-2 | soft | 2 | 48.2 | 47.8 | 48 | NA | NA | NA | NA |
| 20180923 | Pocillopora | 1757 | 198 | hard | NA | NA | NA | NA | 25 | 25 | 25 | 8.3 |
| 20180923 | Pocillopora | 1757 | 198-1 | hard | 1 | 79 | 78.6 | 78.8 | NA | NA | NA | NA |
| 20180923 | Pocillopora | 1757 | 198-2 | hard | 2 | 31.6 | 31.2 | 31.4 | NA | NA | NA | NA |
| 20181103 | Montipora | 2009 | 199 | soft | NA | NA | NA | NA | 20.6 | 20.4 | 20.5 | 5.6 |
| 20181103 | Montipora | 2009 | 199-1 | soft | 1 | 41.2 | 41.4 | 41.3 | NA | NA | NA | NA |
| 20181103 | Montipora | 2009 | 199-2 | soft | 2 | 10.2 | 10.1 | 10.15 | NA | NA | NA | NA |
| 20181103 | Montipora | 2009 | 200 | hard | NA | NA | NA | NA | 11.2 | 11.2 | 11.2 | ** |
| 20181103 | Montipora | 2009 | 200-1 | hard | 1 | 13.5 | 13.5 | 13.5 | NA | NA | NA | NA |
| 20181103 | Montipora | 2009 | 200-2 | hard | 2 | 7.94 | 7.86 | 7.9 | NA | NA | NA | NA |
| 20181103 | Montipora | 1121 | 201 | soft | NA | NA | NA | NA | 20.8 | 20.4 | 20.6 | ** |
| 20181103 | Montipora | 1121 | 201-1 | soft | 1 | 17 | 16.8 | 16.9 | NA | NA | NA | NA |
| 20181103 | Montipora | 1121 | 201-2 | soft | 2 | 6.44 | 6.3 | 6.37 | NA | NA | NA | NA |
| 20181103 | Montipora | 1121 | 202 | hard | NA | NA | NA | NA | 15.6 | 15.4 | 15.5 | ** |
| 20181103 | Montipora | 1121 | 202-1 | hard | 1 | 30 | 30 | 30 | NA | NA | NA | NA |
| 20181103 | Montipora | 1121 | 202-2 | hard | 2 | 5.7 | 5.58 | 5.64 | NA | NA | NA | NA |
| Timepoint | Species | Coral ID | Extraction ID | Homogenization | DNA Elution | DNA Reading 1 | DNA Reading 2 | Average DNA ng/μl | RNA Reading 1 | RNA Reading 2 | Average RNA ng/μl | RIN |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 20181020 | Pocillopora | 2012 | 203 | soft | NA | NA | NA | NA | 46.6 | 46.4 | 46.5 | 8.8 |
| 20181020 | Pocillopora | 2012 | 203-1 | soft | 1 | 42 | 40.6 | 41.3 | NA | NA | NA | NA |
| 20181020 | Pocillopora | 2012 | 203-2 | soft | 2 | 19.1 | 18.7 | 18.9 | NA | NA | NA | NA |
| 20181020 | Pocillopora | 2012 | 204 | hard | NA | NA | NA | NA | 60.8 | 60.4 | 60.6 | 8.7 |
| 20181020 | Pocillopora | 2012 | 204-1 | hard | 1 | 242 | 240 | 241 | NA | NA | NA | NA |
| 20181020 | Pocillopora | 2012 | 204-2 | hard | 2 | 36.2 | 36 | 36.1 | NA | NA | NA | NA |
| 20181020 | Montipora | 1436 | 205 | soft | NA | NA | NA | NA | 14.8 | 14.8 | 14.8 | 9.1 |
| 20181020 | Montipora | 1436 | 205-1 | soft | 1 | 91 | 90.6 | 90.8 | NA | NA | NA | NA |
| 20181020 | Montipora | 1436 | 205-2 | soft | 2 | 16.1 | 16.1 | 16.1 | NA | NA | NA | NA |
| 20181020 | Montipora | 1436 | 206 | hard | NA | NA | NA | NA | ** | ** | ** | ** |
| 20181020 | Montipora | 1436 | 206-1 | hard | 1 | 85.8 | 85.6 | 85.7 | NA | NA | NA | NA |
| 20181020 | Montipora | 1436 | 206-2 | hard | 2 | 9.32 | 9.28 | 9.3 | NA | NA | NA | NA |
| 20180929 | Pocillopora | 1254 | 207 | soft | NA | NA | NA | NA | 49.8 | 49.6 | 49.7 | 8 |
| 20180929 | Pocillopora | 1254 | 207-1 | soft | 1 | 280 | 278 | 279 | NA | NA | NA | NA |
| 20180929 | Pocillopora | 1254 | 207-2 | soft | 2 | 43.4 | 43.2 | 43.3 | NA | NA | NA | NA |
| 20180929 | Pocillopora | 1254 | 208 | hard | NA | NA | NA | NA | 32.8 | 32.6 | 32.7 | 8.5 |
| 20180929 | Pocillopora | 1254 | 208-1 | hard | 1 | 169 | 169 | 169 | NA | NA | NA | NA |
| 20180929 | Pocillopora | 1254 | 208-2 | hard | 2 | 32.8 | 32.6 | 32.7 | NA | NA | NA | NA |
| 20181020 | Pocillopora | 1051 | 209 | soft | NA | NA | NA | NA | 75.8 | 75.6 | 75.7 | 8.3 |
| 20181020 | Pocillopora | 1051 | 209-1 | soft | 1 | 248 | 244 | 246 | NA | NA | NA | NA |
| 20181020 | Pocillopora | 1051 | 209-2 | soft | 2 | 86.4 | 86 | 86.2 | NA | NA | NA | NA |
| 20181020 | Pocillopora | 1051 | 210 | hard | NA | NA | NA | NA | 68.6 | 68.6 | 68.6 | 8.2 |
| 20181020 | Pocillopora | 1051 | 210-1 | hard | 1 | 220 | 220 | 220 | NA | NA | NA | NA |
| 20181020 | Pocillopora | 1051 | 210-2 | hard | 2 | 45.6 | 45.4 | 45.5 | NA | NA | NA | NA |
| 20180923 | Montipora | 1776 | 211 | soft | NA | NA | NA | NA | 24.6 | 24.6 | 24.6 | 8.1 |
| 20180923 | Montipora | 1776 | 211-1 | soft | 1 | 50.4 | 50.2 | 50.3 | NA | NA | NA | NA |
| 20180923 | Montipora | 1776 | 211-2 | soft | 2 | 11.5 | 11.4 | 11.45 | NA | NA | NA | NA |
| 20180923 | Montipora | 1776 | 212 | hard | NA | NA | NA | NA | 15.4 | 15.6 | 15.5 | 9 |
| 20180923 | Montipora | 1776 | 212-1 | hard | 1 | 50.8 | 50.4 | 50.6 | NA | NA | NA | NA |
| 20180923 | Montipora | 1776 | 212-2 | hard | 2 | 10.5 | 10.4 | 10.45 | NA | NA | NA | NA |
| 20180923 | Pocillopora | 2877 | 213 | soft | NA | NA | NA | NA | 129 | 129 | 129 | 7.7 |
| 20180923 | Pocillopora | 2877 | 213-1 | soft | 1 | 394 | 394 | 394 | NA | NA | NA | NA |
| 20180923 | Pocillopora | 2877 | 213-2 | soft | 2 | 130 | 129 | 129.5 | NA | NA | NA | NA |
| 20180923 | Pocillopora | 2877 | 214 | hard | NA | NA | NA | NA | 48.2 | 48.2 | 48.2 | 7.7 |
| 20180923 | Pocillopora | 2877 | 214-1 | hard | 1 | 264 | 262 | 263 | NA | NA | NA | NA |
| 20180923 | Pocillopora | 2877 | 214-2 | hard | 2 | 59.2 | 59 | 59.1 | NA | NA | NA | NA |
| 20180929 | Montipora | 1604 | 215 | soft | NA | NA | NA | NA | 15.8 | 15.8 | 15.8 | 8.5 |
| 20180929 | Montipora | 1604 | 215-1 | soft | 1 | 63.6 | 63.4 | 63.5 | NA | NA | NA | NA |
| 20180929 | Montipora | 1604 | 215-2 | soft | 2 | 8.08 | 8 | 8.04 | NA | NA | NA | NA |
| 20180929 | Montipora | 1604 | 216 | hard | NA | NA | NA | NA | 10 | 10 | 10 | ** |
| 20180929 | Montipora | 1604 | 216-1 | hard | 1 | 36 | 35.8 | 35.9 | NA | NA | NA | NA |
| 20180929 | Montipora | 1604 | 216-2 | hard | 2 | 5.8 | 5.66 | 5.73 | NA | NA | NA | NA |
| 20180929 | Montipora | 2555 | 217 | soft | NA | NA | NA | NA | 10.4 | 10.2 | 10.3 | ** |
| 20180929 | Montipora | 2555 | 217-1 | soft | 1 | 23.4 | 23.2 | 23.3 | NA | NA | NA | NA |
| 20180929 | Montipora | 2555 | 217-2 | soft | 2 | 6.26 | 6.2 | 6.23 | NA | NA | NA | NA |
| 20180929 | Montipora | 2555 | 218 | hard | NA | NA | NA | NA | 13.8 | 13.8 | 13.8 | 8.9 |
| 20180929 | Montipora | 2555 | 218-1 | hard | 1 | 30.4 | 30.4 | 30.4 | NA | NA | NA | NA |
| 20180929 | Montipora | 2555 | 218-2 | hard | 2 | 6.66 | 6.6 | 6.63 | NA | NA | NA | NA |
| 20180923 | Montipora | 1583 | 219 | soft | NA | NA | NA | NA | 11.2 | 11.2 | 11.2 | ** |
| 20180923 | Montipora | 1583 | 219-1 | soft | 1 | 49 | 48.8 | 48.9 | NA | NA | NA | NA |
| 20180923 | Montipora | 1583 | 219-2 | soft | 2 | 7.44 | 7.38 | 7.41 | NA | NA | NA | NA |
| 20180923 | Montipora | 1583 | 220 | hard | NA | NA | NA | NA | ** | ** | ** | ** |
| 20180923 | Montipora | 1583 | 220-1 | hard | 1 | 32.6 | 32.4 | 32.5 | NA | NA | NA | NA |
| 20180923 | Montipora | 1583 | 220-2 | hard | 2 | 5.3 | 5.04 | 5.17 | NA | NA | NA | NA |
| 20180929 | Pocillopora | 1466 | 221 | soft | NA | NA | NA | NA | 58.8 | 58.8 | 58.8 | 8.3 |
| 20180929 | Pocillopora | 1466 | 221-1 | soft | 1 | 308 | 306 | 307 | NA | NA | NA | NA |
| 20180929 | Pocillopora | 1466 | 221-2 | soft | 2 | 55 | 54.6 | 54.8 | NA | NA | NA | NA |
| 20180929 | Pocillopora | 1466 | 222 | hard | NA | NA | NA | NA | 61.2 | 61.2 | 61.2 | 7.8 |
| 20180929 | Pocillopora | 1466 | 222-1 | hard | 1 | 196 | 196 | 196 | NA | NA | NA | NA |
| 20180929 | Pocillopora | 1466 | 222-2 | hard | 2 | 32.8 | 32.8 | 32.8 | NA | NA | NA | NA |
| 20180929 | Montipora | 2016 | 223 | soft | NA | NA | NA | NA | 10.8 | 10.8 | 10.8 | ** |
| 20180929 | Montipora | 2016 | 223-1 | soft | 1 | 22 | 21.8 | 21.9 | NA | NA | NA | NA |
| 20180929 | Montipora | 2016 | 223-2 | soft | 2 | 5.2 | 5.14 | 5.17 | NA | NA | NA | NA |
| 20180929 | Montipora | 2016 | 224 | hard | NA | NA | NA | NA | ** | ** | ** | ** |
| 20180929 | Montipora | 2016 | 224-1 | hard | 1 | 26.4 | 26.4 | 26.4 | NA | NA | NA | NA |
| 20180929 | Montipora | 2016 | 224-2 | hard | 2 | 4.36 | 4.32 | 4.34 | NA | NA | NA | NA |
| 20180923 | Montipora | 1321 | 225 | soft | NA | NA | NA | NA | ** | ** | ** | ** |
| 20180923 | Montipora | 1321 | 225-1 | soft | 1 | 45.4 | 45.4 | 45.4 | NA | NA | NA | NA |
| 20180923 | Montipora | 1321 | 225-2 | soft | 2 | 6.42 | 6.38 | 6.4 | NA | NA | NA | NA |
| 20180923 | Montipora | 1321 | 226 | hard | NA | NA | NA | NA | ** | ** | ** | ** |
| 20180923 | Montipora | 1321 | 226-1 | hard | 1 | 28.6 | 28.6 | 28.6 | NA | NA | NA | NA |
| 20180923 | Montipora | 1321 | 226-2 | hard | 2 | 6.7 | 6.62 | 6.66 | NA | NA | NA | NA |
Fragment #2300 is very bleached with algae on the top of some of the branches. Pieces taken from the no algae portions.
Link to 20190731 TapeStation report, Extractions #179-202
Several samples did not sink into the well. Possibly because of excess ethanol.
Written on July 31, 2019