User:Tara K. Luckau/Notebook/Team ConGen/2012/01/06

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==CNHY Acos5==
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==ASHY Multiplex==
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===PCR===
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* prepping to start multiplexing CNHY primers ... so see primer interactions ...
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* [[Image:20111023_PCRa.png|800 px]]
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===Gel===
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===Gradient Summary===
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{| {{table}} style="text-align: center"
 
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|-
 
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! Pour !! Load !! Run
 
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|-
 
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| 270 mL 1x TAE + 5.4 g agarose || 2 µL gel load dye + 4 µL PCR product || 160 V
 
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|-
 
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| 27 µL GelRed || 6 µL ladder || 45 minutes
 
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|}
 
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* green cells indicate clean amplification; orange cells indicate less-than-ideal conditions, but useable if necessary
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* [[Image:20120106 GradientSummary.png]]
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[[Image:20111023_Gel.png|800 px]]
 
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* mispriming everywhere - primer pair not usable for CNHY
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===Multiplex Map===
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* lots of mispriming, but may be able to use conditions indicated by orange face ([[Image:orangefrownyface.png|20 px]]), if needed, under stringent conditions
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* favorable conditions indicated by [[Image:greenhappyface.png|25 px]]
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* markers placed arbitrarily
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* marker ranges indicated as in Crawford et al 2007, but approximate amplicon size may be given in final parentheses if Crawford designation is wide or very different from gel.
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* [[Image:20120106 Map.png]]
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===AutoDimer===
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* color families (red, green, blue, gray) indicate possible multiplexing based on primer interactions
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* [[Image:20120106_AutoDimer.png|800 px]]
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===PCR - determine approximate range of each marker===
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* pool high-quant DNA samples from throughout SD county:
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:-- CNHY CPN 02
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:-- CNHY LOM 08
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:-- CNHY RAJ 01
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:-- CNHY RAJ 35
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:-- CNHY RAJ 42
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:-- CNHY RAJ 50
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:-- CNHY TP1 11
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:-- CNHY TP3 05
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:-- CNHY TP3 19
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:-- CNHY TP3 20
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* 2µL each DNA STK + 80µL LowTE (to dilute to ~10ng/µL) + 20µL CNHY 062911TKLH ('play' DNA, already 10 ng/µL)
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* [[Image:20120106_PCR.png|800 px]]
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Contents


ASHY Multiplex

  • prepping to start multiplexing CNHY primers ... so see primer interactions ...


Gradient Summary

  • green cells indicate clean amplification; orange cells indicate less-than-ideal conditions, but useable if necessary
  • Image:20120106 GradientSummary.png


Multiplex Map

  • markers placed arbitrarily
  • marker ranges indicated as in Crawford et al 2007, but approximate amplicon size may be given in final parentheses if Crawford designation is wide or very different from gel.
  • Image:20120106 Map.png


AutoDimer

  • color families (red, green, blue, gray) indicate possible multiplexing based on primer interactions


PCR - determine approximate range of each marker

  • pool high-quant DNA samples from throughout SD county:
-- CNHY CPN 02
-- CNHY LOM 08
-- CNHY RAJ 01
-- CNHY RAJ 35
-- CNHY RAJ 42
-- CNHY RAJ 50
-- CNHY TP1 11
-- CNHY TP3 05
-- CNHY TP3 19
-- CNHY TP3 20
  • 2µL each DNA STK + 80µL LowTE (to dilute to ~10ng/µL) + 20µL CNHY 062911TKLH ('play' DNA, already 10 ng/µL)





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