Narragansett Bay Adult Oyster DNA Sonication with 50 new samples
Sonication of oyster DNA samples for shearing to 150 bp
DNA extraction was previously performed on 50 oysters collected from 5 sites in Narragansett Bay.
Sonication
Samples were sonicated using the Qsonica Protocol.
All 50 samples were sonicated to ~150 basepairs. Sonication was completed across 4 different days:
- Apr. 21, 2021: 8 samples
- Apr. 23, 2021: 14 samples
- Apr. 24, 2021: 14 samples
- Apr. 26, 2021: 14 samples
April 21, 2021
| Sample | Aliquot (for 500ng DNA) | 10 mM Tris HCl pH 8 to 51 uL (1 extra uL for TapeStation) |
|---|---|---|
| NAR_8 (1.8) | 34.25 | 16.75 |
| NAR_9 (1.9) | 23.15 | 27.85 |
| GHP_6 (2.6) | 30.67 | 20.33 |
| BAR_2 (3.2) | 41.32 | 9.68 |
| BAR_8 (3.8) | 31.85 | 19.15 |
| KIC_4 (4.4) | 35.46 | 15.54 |
| KIC_8 (4.8) | 24.27 | 26.73 |
| MCD_5 (5.5) | 14.53 | 36.47 |
Samples were sonicated with:
- 32 minute time setting
- 15 seconds on 15 seconds off
- amplitude of 25%
Samples were spun down every 2 minutes of the program (the timer pauses during the 15 second OFF period, so while 4 actual minutes pass only 2 minutes pass in the program).
Samples were checked following the D5000 Tape Station Protocol.
Report can be accessed here
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Samples 1.9, 2.6, 3.2, 3.8, and 4.8 were sonicated for 6 more minutes and again checked on the Tape Station.
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On April 22, 2021, samples 2.6, 3.2, 3.8, and 4.8 were sonicated for 12 more minutes and checked on the Tape Station.
April 23, 2021
| Sample | Aliquot (for 500ng DNA) | 10 mM Tris HCl pH 8 to 51 uL (1 extra uL for TapeStation) |
|---|---|---|
| NAR_4 (1.4) | 25.13 | 25.87 |
| NAR_10 (1.10) | 30.12 | 20.88 |
| GHP_1 (2.1) | 31.75 | 19.25 |
| GHP_3 (2.3) | 50.00 | 1.00 |
| GHP_5 (2.5) | 6.22 | 44.78 |
| GHP_10 (2.10) | 16.45 | 34.55 |
| BAR_3 (3.3) | 4.85 | 46.15 |
| BAR_6 (3.6) | 4.81 | 46.19 |
| BAR_9 (3.9) | 8.39 | 42.61 |
| KIC_7 (4.7) | 43.86 | 7.14 |
| KIC_9 (4.9) | 35.97 | 15.03 |
| MCD_1 (5.1) | 17.24 | 33.76 |
| MCD_2 (5.2) | 5.00 | 46.00 |
| MCD_7 (5.7) | 51.00 | 0.00 |
Samples were sonicated with:
- 36 minute time setting
- 15 seconds on 15 seconds off
- amplitude of 25%
Samples were spun down every 2 minutes of the program
Samples were checked following the D5000 Tape Station Protocol.
Report can be accessed here.
April 24, 2021
| Sample | Aliquot (for 500ng DNA) | 10 mM Tris HCl pH 8 to 51 uL (1 extra uL for TapeStation) |
|---|---|---|
| NAR_1 (1.1) | 34.48 | 16.52 |
| NAR_3 (1.3) | 40.00 | 11.00 |
| NAR_6 (1.6) | 30.70 | 20.30 |
| GHP_4 (2.4) | 6.07 | 44.93 |
| GHP_8 (2.8) | 5.83 | 45.17 |
| BAR_1 (3.1) | 45.45 | 5.55 |
| BAR_4 (3.4) | 8.83 | 42.17 |
| BAR_10 (3.10) | 51.00 | 0.00 |
| KIC_2 (4.2) | 10.73 | 40.27 |
| KIC_5 (4.5) | 26.18 | 24.82 |
| KIC_6 (4.6) | 29.07 | 21.93 |
| MCD_4 (5.4) | 12.20 | 38.80 |
| MCD_6 (5.6) | 42.02 | 8.98 |
| MCD_9 (5.9) | 4.42 | 46.58 |
Samples were sonicated with:
- 36 minute time setting
- 15 seconds on 15 seconds off
- amplitude of 25%
Samples were spun down every 2 minutes of the program
Samples were checked following the D5000 Tape Station Protocol.
Report can be accessed here.
April 26, 2021
| Sample | Aliquot (for 500ng DNA) | 10 mM Tris HCl pH 8 to 51 uL (1 extra uL for TapeStation) |
|---|---|---|
| NAR_2 (1.2) | 30.30 | 20.70 |
| NAR_5 (1.5) | 30.50 | 20.50 |
| NAR_7 (1.7) | 31.00 | 20.00 |
| GHP_2 (2.2) | 50.00 | 1.00 |
| GHP_7 (2.7) | 32.26 | 18.74 |
| GHP_9 (2.9) | 16.78 | 34.22 |
| BAR_5 (3.5) | 7.04 | 43.96 |
| BAR_7 (3.7) | 38.76 | 12.24 |
| KIC_1 (4.1) | 13.89 | 37.11 |
| KIC_3 (4.3) | 4.95 | 46.05 |
| KIC_10 (4.10) | 51.00 | 0.00 |
| MCD_3 (5.3) | 5.90 | 45.10 |
| MCD_8 (5.8) | 26.46 | 24.54 |
| MCD_10 (5.10) | 8.45 | 42.55 |
Samples were sonicated with:
- 36 minute time setting
- 15 seconds on 15 seconds off
- amplitude of 25%
Samples were spun down every 2 minutes of the program
Samples were checked following the D5000 Tape Station Protocol.
Report can be accessed here.