Using Tapestation to evaluate size distribution, integrity of 1800s re-extractions. Will also run some old extractions to check whether they’ve degraded since first being extracted.
This time since I expect my 1800s samples to have essentially no HMW DNA, will use an HS D5000 tape instead of a gDNA tape.
HS D5000 tape requires 2uL of DNA sample. I want to conserve my extractions, and the HS D5000 tape can handle very low concentrations, so I’ll be using a 2x dilution for all samples (1uL extraction + 1uL Zymo EB)
Followed HS D5000 protocol found here.
Tapestation layout:
| 1 | 2 | |
|---|---|---|
| A | Ladder | 1740363 |
| B | 50368 (new) | 51892 |
| C | 50603 (new) | 51732 |
| D | 19054 (new) | 14399 |
| E | 14399 (new) | 50368 |
| F | 42137 (new) | 50603 |
| G | 1606826 | |
| H | 1740336 |
Notes:
Looks like 50368 (new), 42137 (new), and 14399 (new) are by far the best 1800s re-extractions to use for sequencing.
Don’t see an immediately obvious degradation issue comparing new to old extractions of 50368, 50603, 14399, will need to compare to OG tapestation.