Soft and Hard Homogenization Extractions

Soft and Hard Homogenization DNA/RNA Extractions #343-350

20190814 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).

Coral fragments were randomly chosen from different timepoint bags.

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

DNA Standard 1: 185.60 ng/μl
DNA Standard 2: 20,540.05 ng/μl
RNA Standard 1: 386.59 ng/μl
RNA Standard 2: 10,597.72 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 Pocillopora 2072 343 soft 41.4 41.2 41.3 59.6 59.6 59.6 6.6
20181006 Pocillopora 2072 344 hard 20.2 20.2 20.2 24.6 24.6 24.6 NA
20180929 Montipora 1317 345 soft 19.2 19.1 19.15 23.4 23.4 23.4 7.7
20180929 Montipora 1317 346 hard 12.2 12.1 12.15 14.4 14.4 14.4 NA
20180922 Pocillopora 1043 347 soft 43.8 43.8 43.8 55 55.2 55.1 8.1
20180922 Pocillopora 1043 348 hard 26 25.8 25.9 37.6 37.8 37.7 NA
20180922 Pocillopora 1343 349 soft 23.8 23.8 23.8 33.2 33.4 33.3 8.4
20180922 Pocillopora 1343 350 hard 11.7 11.7 11.7 24.6 24.6 24.6 NA

Link to 20190814 TapeStation report, Extractions #343-350

Gel Electrophoresis Results:

20190814 Extractions #343-350

Written on August 14, 2019