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

Tara's Lab Notebook

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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