Soft and Hard Homogenization Extractions

Soft and Hard Homogenization DNA/RNA Extractions #53-72

20190722 and 20190723 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.
Coral fragments were randomly chosen from different timepoint bags.

Timepoint Species Coral ID Extraction ID Homgenization
20181020 Pocillopora 1459 53 soft
20181020 Pocillopora 1459 54 hard
20180922 Montipora 2021 55 soft
20180922 Montipora 2021 56 hard
20181103 Montipora 1420 57 soft
20181103 Montipora 1420 58 hard
20181103 Pocillopora 2979 59 soft
20181103 Pocillopora 2979 60 hard
20181117 Montipora 1689 61 soft
20181117 Montipora 1689 62 hard
20180922 Montipora 1628 63 soft
20180922 Montipora 1628 64 hard
20181020 Pocillopora 2513 65 soft
20181020 Pocillopora 2513 66 hard
20181020 Montipora 1235 67 soft
20181020 Montipora 1235 68 hard
20181103 Pocillopora 1141 69 soft
20181103 Pocillopora 1141 70 hard
20181117 Montipora 1332 71 soft
20181117 Montipora 1332 72 hard

Fragment Prep start 10:03 end 10:38
Soft/Hard homogenization start 10:39 end 11:39
P2513 tips covered in algae, hard to get good fragment pieces. Extractions start 11:40 end 14:50

Qubit Results:

DNA (ng/μl)        
Standard 1 199.52      
Standard 2 22606.02      
Coral ID Extraction ID Reading 1 Reading 2 Average
1459 53 57.4 57 57.2
1459 54 too low too low **
2021 55 25.2 25 25.1
2021 56 13.9 13.5 13.7
1420 57 3.26 3.22 3.24
1420 58 9.72 9.54 9.63
2979 59 19.2 19 19.1
2979 60 35.2 35.2 35.2
1689 61 too low too low **
1689 62 4.08 3.88 3.98
1628 63 8.1 8.06 8.08
1628 64 4.74 4.7 4.72
2513 65 23 22.8 22.9
2513 66 12.6 12.5 12.55
1235 67 2.7 2.62 2.66
1235 68 4.7 4.7 4.7
1141 69 17 16.9 16.95
1141 70 24.2 24 24.1
1332 71 too low too low **
1332 72 2.24 2.2 2.22
RNA (ng/μl)        
Standard 1 402.17      
Standard 2 12659.11      
Coral ID Extraction ID Reading 1 Reading 2 Average
1459 53 57 56.4 56.7
1459 54 33.6 33.6 33.6
2021 55 10 10 10
2021 56 10.6 10.6 10.6
1420 57 ** ** **
1420 58 ** ** **
2979 59 36.4 36.4 36.4
2979 60 26 26 26
1689 61 ** ** **
1689 62 ** ** **
1628 63 10.6 10.6 10.6
1628 64 10.2 10.2 10.2
2513 65 31.2 31.2 31.2
2513 66 22 22 22
1235 67 ** ** **
1235 68 ** ** **
1141 69 47.2 47.2 47.2
1141 70 25.4 25.4 25.4
1332 71 ** ** **
1332 72 ** ** **

Qubit re-done for following samples:

DNA (ng/μl)        
Standard 1 169.47      
Standard 2 18543.03      
Coral ID Extraction ID Reading 1 Reading 2 Average
1459 53 62.2 60.6 61.4
1459 54 42.6 41.6 42.1
DNA (ng/μl)        
Standard 1 209.93      
Standard 2 23170.52      
Coral ID Extraction ID Reading 1 Reading 2 Average
2979 59 36.8 36.6 36.7
2979 60 25 25 25
1689 61 6.3 6.28 6.29
1689 62 6.46 6.42 6.44
1141 69 45 45 45
1141 70 27.8 27.8 27.8
RNA (ng/μl)        
Standard 1 411.38      
Standard 2 12375.27      
Coral ID Extraction ID Reading 1 Reading 2 Average
1459 53 56.6 56.6 56.6
1459 54 34.8 35 34.9
2979 59 46 46 46
2979 60 29.4 29.4 29.4
1689 61 ** ** **
1689 62 ** ** **
1141 69 41 41 41
1141 70 29.2 29.2 29.2

Gel Electrophoresis Results:

Extraction #53-68: 20190723

Extraction #69-82: 20190723

TapeStation Results:

Coral Fragment ID Extraction ID RIN
1459 53 7
1459 54 6.9
2021 55 **
2021 56 8.1
1420 57 **
1420 58 **
2979 59 7.6
2979 60 6.8
1689 61 **
1689 62 **
1628 63 **
1628 64 **
2513 65 6.7
2513 66 6.5
1235 67 **
1235 68 **
1141 69 7.3
1141 70 7
1332 71 **
1332 72 8.1

Link to 20190723 report #1, Extractions #53-67
Link to 20190723 report #2, Extractions #68-82

Written on July 22, 2019