User:Tara K. Luckau/Notebook/Team ConGen/2011/10/21

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CNHY Acos5


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

  • stuff


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_15_TP1a
Scun3 - 0.15 µL
Scun11 - 0.2 µL
sar80 - 0.2 µL

  • Scun11_25_SYRa
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
Image:20111021 AutoDimer.png

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