Soft and Hard Homogenization Extractions

20191001 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: 163.56 ng/μl
DNA Standard 2: 22,644.53 ng/μl
RNA Standard 1: 402.39 ng/μl
RNA Standard 2: 10,030.67 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 Montipora 2511 485 soft 10.2 9.92 10.06 19.8 19.4 19.6 9.2
20181215 Montipora 2511 486 hard 7.62 7.52 7.57 12.2 12 12.1 NA
20181215 Montipora 2188 487 soft 17.7 17.5 17.6 13.4 13.4 13.4 9.2
20181215 Montipora 2188 488 hard 10.3 10.2 10.25 10.2 10.2 10.2 NA
20181215 Pocillopora 2668 489 soft 28.4 28.2 28.3 90.6 90.6 90.6 9
20181215 Pocillopora 2668 490 hard 31.4 31.2 31.3 52.6 52.4 52.5 NA
20181215 Montipora 2302 491 soft 12.3 12.2 12.25 17.6 17.8 17.7 8.7
20181215 Montipora 2302 492 hard 8.74 8.64 8.69 11.2 11.2 11.2 NA
20181215 Montipora 1248 493 soft 15.5 15.4 15.45 14.4 14.4 14.4 **
20181215 Montipora 1248 494 hard 6.46 6.38 6.42 13.8 13.6 13.7 NA

Link to 20191001 TapeStation report, Extractions #485-494

Gel Electrophoresis Results:

20191001 Extractions #485-494

Written on October 1, 2019