All numbers in ng/uL (equivelantly ug/mL). Original volume is 1 mL so this equivelantly DNA mass.
Though some samples were split multiple ways, EtOH is 2:1 with vs without glycogen. Filtration was done with 150 uL of 1 mL PCR.
| Sample | PCR ng/uL | Filtration | EtOH | EtOH no glyc |
|---|---|---|---|---|
| #1 Y nick | 41.8 | N/A | 36 | 37 |
| #2 B nick | 26.4 | N/A | 21 | 14 |
| #3 ubx nick | 24.1 | N/A | 39 | 0* |
| #4 Y PPT | 21.8 | 7.95 | 25.3 | 14 |
| #5 Y CPPT | 26.6 | 8.85 | 31 | 13 |
pipetting 1 uL into an empty tube (rather than into solution) is inaccurate…
For most samples, the glycogen precipitation came out higher yield.
Conclusions
- Filtering has lower yield, dramatically worse spectra on the nano-drop, and bad subsequent behavior of DNA on the gel.
- Extra full length adapter primer is better than extra short adapter primer. Could try changing temperature lower to optimize this.
- Glycogen has some adventages still on the meso-scale
Nanodrop of filtered samples
- L after filter = ~16 ng/uL (very ugly, ddH2O blank). 18 ng/uL (
- #4 filtered 25 ng/ul, very ugly
- #5 filtered 35 ng/uL very ugly, shoulder on a downward slope.
qubit
- #1 41.8 (in 1 mL)
- #2 26.4
- #3 24.1
- #4 21.8
- #5 26.6
- #6 .10 ug/mL
- #7 25.4
- #8 32.0
- #9 21.7
- #1 EtOH 39.8 (1:10) in 30 uL *3
- #2 EtOH 23.3
- #3 EtOH 38.8
- #4 EtOH 23.9
- #5 EtOH 30,0
- #1 EtOH no glyc 41.6
- #2 EtOH no glyc 16.6
- #3 EtOH no glyc .14
- #4 EtOH no glyc 13.2
- #5 EtOH no glyc 12.8
- #4 filtered 7.95 ug/mL in 150 uL. used 150 uL of 1 mL PCR
- #5 filtered 8.85 ug/mL in 150 uL
- ladder filtered 5.61 ug/mL in 150 uL
- ladder unfiltered in 1 mL 4.31 ug/mL