User:Tara K. Luckau/Notebook/Team ConGen/2011/11/02

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Contents


CNHY Ai5037

PCR


Gel

Pour Load Run
270 mL 1x TAE + 5.4 g agarose 2 µL gel load dye + 4 µL PCR product 160 V
27 µL GelRed 6 µL ladder 45 minutes


  • favorable conditions indicated by


Meeting with Bohonak

Proposal stuff

  • overall, what I have right now is sufficient for a proposal, so long as I can defend the remainder of the work
  • some tables:
one with loci (each species) ... # proposed, # potential, # screened, # polymorphic, # polymorphic/need cleaning, # monomorphic/dirty/throw out
one with tissue (each species / location) ... # proposed, # captured, # extracted
  • mendelian inheritance of markers:
families
if not, then gravid female
if not, then H-W equilibrium (and the thing from Genelex), with defense of why this is good enough
  • calculation of error rates:
present a plan for calculation
some citations from Justin's: Hoffman and Amos; Bonin et al 2004
handful of samples re-extracted, re-amplified, re-scored throughout the process (not all at the end)
because of human error, null alleles
  • lay out a plan for hypothesis testing
for hypothesis 1, here are the three analyses I'll be using
for hypothesis 2, here are the three analyses I'll be using
  • be able to talk about assumptions of each analysis program
popgen knowledge should be sufficient
familiarize with each individual program


CNHY Ai5042

PCR



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