Qubit e5 samples
Qubit w/ e5 timeseries DNA samples
We are sending out the e5 timeseries DNA samples for WBGS but some samples still have low concentrations. There are ~20 samples that have <200 ng of DNA (see spreadsheet here; mostly POR). There are 10 samples that had too low concentration for Qubit. I’m going to re-Qubit these 20 samples with the HS Qubit kit to get a better idea of concentrations.
Note: All samples except for 20240805_POC-52_TP1 are POR.
| SampleName | QC_Number | DNA1_ng_uL | DNA2_ng_uL | DNA_Average | DNA_uL | DNA_ng |
|---|---|---|---|---|---|---|
| 7-20220208 | 1 | 0.0604 | 0.0632 | 0.0618 | 82 | 5.0676 |
| 195 | 2 | 0.0632 | 0.0624 | 0.0628 | 85 | 5.338 |
| 749 | 3 | 0.448 | 0.287 | 0.3675 | 85 | 31.2375 |
| 557 | 4 | 0.116 | 0.0892 | 0.1026 | 85 | 8.721 |
| 637 | 5 | 0.305 | 0.293 | 0.299 | 85 | 25.415 |
| 247-20220208 | 6 | 0.102 | 0.0912 | 0.0966 | 85 | 8.211 |
| 13 | 7 | 0.121 | 0.106 | 0.1135 | 82 | 9.307 |
| 469-20211122 | 8 | 0.334 | 0.334 | 0.334 | 82 | 27.388 |
| 251-20220208 | 9 | 0.118 | 0.104 | 0.111 | 85 | 9.435 |
| 20240805_POC-52_TP1 | 10 | 0.11 | 0.101 | 0.1055 | 85 | 8.9675 |
| 235 | 11 | 1.4 | 1.4 | 1.4 | 82 | 114.8 |
| 23 | 12 | 0.222 | 0.204 | 0.213 | 85 | 18.105 |
| 711 | 13 | 0.848 | 0.84 | 0.844 | 85 | 71.74 |
| 327 | 14 | 0.391 | 0.375 | 0.383 | 85 | 32.555 |
| 491 | 15 | 0.432 | 0.448 | 0.44 | 85 | 37.4 |
| 669 | 16 | 0.808 | 0.8 | 0.804 | 85 | 68.34 |
| 477 | 17 | 0.272 | 0.272 | 0.272 | 85 | 23.12 |
| 493 | 18 | 0.508 | 0.5 | 0.504 | 85 | 42.84 |
| 515-20211104 | 19 | 0.324 | 0.323 | 0.3235 | 85 | 27.4975 |
| 529 | 20 | 0.308 | 0.304 | 0.306 | 85 | 26.01 |
Not great. 7 samples have <10 ng of DNA, and 19 samples have <100 ng of DNA. Azenta said: “Our lab prefers to have at least ~300ng of input DNA given our internal workflow optimizations. For samples under 200ng or so, we can proceed at best-efforts. Like I said, we have a lot of experience working with less-than-optimal samples and often see good results with starting materials as low as 10ng. However, if you were able to re-extract and/or pool samples to have more starting material, that would be a good option.”
Options moving forward
- Send as-is and hope Azenta can successfully library prep
- Re-extract samples that have <200ng to see if we can get higher concentrations
- Pool samples to get to higher concentrations