|
CNHY Acos5
Gel
| Pour |
Load |
Run
|
| 270 mL 1x TAE + 5.4 g agarose |
2 µL gel load dye + 4 µL PCR product |
80 V
|
| 27 µL GelRed |
6 µL ladder |
90 minutes
|
SCOC MP1
Fragment Analysis
Summary of fragment analysis results
- Numbers indicate intensity of peak for each marker (or average of peaks, if heterozygous)
- At bottom, indicates ratio of each lane
- Yellow - Scun3:Scun11:sar80 intensity
- Here, average of intensity for column (rounded to nearest hundred), and ratio
Best conditions
- Scun3 - 0.15 µL
- Scun11 - 0.2 µL
- sar80 - 0.2 µL
- Scun3 - 0.2 µL
- Scun11 - 0.25 µL
- sar80 - 0.2 µL
- sar80_30_TP1a (but sar80 usually did not amplify to detectable levels)
- Scun3 - 0.2 µL
- Scun11 - 0.2 µL
- sar80 - 0.3 µL
Conclusions and Next Steps
- sar80 barely amplified, if at all
- in primer dimers, reverse (with pigtail) dimerizes with forward
- could try reverse without pigtail (would decrease nucleotide matches from 9 to 5)
- could try sar80 in blue lane (no dimers in blue lane) (shift Scun15 from green to yellow; shift Scun16 from blue to green)
- AutoDimer with all 10 primer pairs for SCOC MP1
|
Tara's Lab Notebook
