User:Tara K. Luckau/Notebook/Team ConGen/2012/07/23

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Contents


Frag Results

  • UAGC Code: WGAC


SCOC MP1

SCOC MP1 G+Y

  • tried to combine SCOC MP1-G (Scun9, Scun15, Scun19) with SCOC MP1-Y (Scun3, Scun11)



  • another locus showed up outta nowhere! (green lane, ~200bp amplicon)
looks like a real microsatellite, with adenylated bump, downward slope between the two peaks of heterozygote individuals (though very steep), and leading peaks
  • leave MP1-G and MP1-Y separate
  • READY TO RUN ALL SCOC SAMPLES FOR THESE 9 MARKERS!


CNHY/TI MP1 Uniplex

Ai5033 - 165-175

  • first uniplex for this marker did not amplify, but previous gels indicated it should be a good, clean marker; re-ran frag uniplex



  • nice peaks for CNHY samples
  • multiple peaks for CNTI samples - not a good marker for this species/temperature/[MgCl2]


CNHY/TI MP1

  • primer pairs grouped into two multiplexes based on primer interactions, annealing temperature, amplicon size; all primers at same concentration
  • let's just try these multiplexes and tweak parameters from there


MP1a





CNHY/TI
Ai5043 did not amplify
Acos3 amplified well; no changes needed
Acos5 amplified with high intensity, pull down a bit
Ai5013 amplified with very low intensity; increase concentration
Ai5071 amplified with lower intensity; increase a bit


  • otherwise, clean multiplex with limited errant peaks; a bit of bleed through, but easily recognizable
  • just work on more consistent peak height and Ai5043


MP1b





  • multiplex runs differently depending on species:


CNHY CNTI
Ai5033 amplified well; no changes needed did not amplify
Ai5057 did not amplify did not amplify
Ai5037 amplified well; no changes needed amplified well; no changes needed
Ai5035 amplified well; no changes needed amplified well but with low intensity, increase concentration a bit
Ai5062 amplified but with very low intensity; increase concentration amplified well; no changes needed


  • otherwise, clean multiplex with limited errant peaks; a bit of bleed through, but easily recognizable
  • will need to adjust PCR parameters separately for each species


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